Back to Long Tests report for BioC 3.22

This page was generated on 2025-09-06 23:55 -0400 (Sat, 06 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4618
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 7/29HostnameOS / ArchCHECK
biodbNcbi 1.13.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-09-06 09:55 -0400 (Sat, 06 Sep 2025)
git_url: https://git.bioconductor.org/packages/biodbNcbi
git_branch: devel
git_last_commit: ad86d6a
git_last_commit_date: 2025-07-24 10:47:22 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbNcbi on lconway

To the developers/maintainers of the biodbNcbi package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biodbNcbi
Version: 1.13.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.13.1.tar.gz
StartedAt: 2025-09-06 16:01:04 -0400 (Sat, 06 Sep 2025)
EndedAt: 2025-09-06 16:01:57 -0400 (Sat, 06 Sep 2025)
EllapsedTime: 53.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNcbi.Rcheck
Warnings: NA

Tests output

biodbNcbi.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNcbi")
Loading required package: biodbNcbi
biodb.INFO [2025-09-06 16:01:49.162][biodb::testContext]
biodb.INFO [2025-09-06 16:01:49.165][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-06 16:01:49.166][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2025-09-06 16:01:49.167][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-06 16:01:49.168][biodb::testContext]
biodb.INFO [2025-09-06 16:01:49.173][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-09-06 16:01:49.174][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-09-06 16:01:49.179][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:01:49.180][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-06 16:01:49.181][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-06 16:01:49.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.184][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-06 16:01:49.197][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-06 16:01:49.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.201][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-06 16:01:49.201][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-06 16:01:49.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.204][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-06 16:01:49.205][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-06 16:01:49.206][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-06 16:01:49.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.208][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-06 16:01:49.210][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-06 16:01:49.210][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-06 16:01:49.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.213][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-06 16:01:49.214][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-06 16:01:49.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.217][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-06 16:01:49.218][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-06 16:01:49.219][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-06 16:01:49.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.222][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-06 16:01:49.223][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-06 16:01:49.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.226][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-06 16:01:49.227][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-06 16:01:49.228][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-06 16:01:49.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.231][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-06 16:01:49.232][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-06 16:01:49.232][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-06 16:01:49.233][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-06 16:01:49.234][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-06 16:01:49.235][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-06 16:01:49.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.238][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-06 16:01:49.239][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-06 16:01:49.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.242][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-06 16:01:49.242][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-06 16:01:49.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.246][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-06 16:01:49.247][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-06 16:01:49.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.250][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-06 16:01:49.250][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-06 16:01:49.252][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-06 16:01:49.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.255][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-06 16:01:49.256][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-06 16:01:49.274][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-06 16:01:49.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.277][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-06 16:01:49.283][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-06 16:01:49.284][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-06 16:01:49.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.289][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-06 16:01:49.315][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:49.327][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-09-06 16:01:49.328][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.328][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:49.329][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.330][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.331][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:49.332][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.332][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-06 16:01:49.333][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:49.334][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.335][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-06 16:01:49.335][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:49.336][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:49.337][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.338][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:01:49.338][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:01:49.338][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:01:49.338][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-06 16:01:49.338][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-06 16:01:49.339][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:01:49.340][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:49.340][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:49.341][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:49.342][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:49.343][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:49.344][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.345][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:49.345][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:49.346][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:49.347][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:49.348][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:49.349][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-06 16:01:49.350][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:49.351][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-06 16:01:49.352][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.353][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:49.353][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.354][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.355][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:49.356][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.357][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-06 16:01:49.357][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:49.358][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.359][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-06 16:01:49.360][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:49.361][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:49.361][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.362][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:01:49.362][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:01:49.362][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:01:49.362][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-06 16:01:49.362][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-06 16:01:49.363][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:01:49.364][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:49.364][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:49.365][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:49.366][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:49.367][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:49.368][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.368][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:49.369][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:49.370][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:49.371][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:49.371][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:49.373][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-06 16:01:49.374][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.375][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-09-06 16:01:49.376][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.377][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:49.377][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.378][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.379][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:49.380][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.381][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-06 16:01:49.381][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:49.382][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:49.383][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-06 16:01:49.384][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:49.384][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:49.385][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.386][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:49.386][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:01:49.387][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:49.388][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:49.389][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:49.390][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:49.390][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:49.391][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.392][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:49.392][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:49.393][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:49.394][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:49.395][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:49.395][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-06 16:01:49.397][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.398][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-06 16:01:49.398][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.399][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:49.400][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.400][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.401][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:49.402][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.403][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-06 16:01:49.404][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:49.405][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:49.405][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-06 16:01:49.406][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:49.407][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:49.408][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.409][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:49.410][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:01:49.411][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:49.411][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:49.412][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:49.413][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:49.414][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:49.415][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.415][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:49.416][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:49.417][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:49.418][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:49.418][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:49.426][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:01:49.426][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.484][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-06 16:01:49.488][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-06 16:01:49.489][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-06 16:01:49.490][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-06 16:01:49.491][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-06 16:01:49.492][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-06 16:01:49.493][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-06 16:01:49.495][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-06 16:01:49.496][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-06 16:01:49.497][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-06 16:01:49.498][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-06 16:01:49.499][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-06 16:01:49.500][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-06 16:01:49.501][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-06 16:01:49.502][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-06 16:01:49.503][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-06 16:01:49.504][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-06 16:01:49.505][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-06 16:01:49.506][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-06 16:01:49.507][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-06 16:01:49.508][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-06 16:01:49.509][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-06 16:01:49.511][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-06 16:01:49.512][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-06 16:01:49.513][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-06 16:01:49.514][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-06 16:01:49.515][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-06 16:01:49.516][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-06 16:01:49.517][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-06 16:01:49.518][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-06 16:01:49.519][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-06 16:01:49.520][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-06 16:01:49.521][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-06 16:01:49.522][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-06 16:01:49.524][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-06 16:01:49.525][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-06 16:01:49.526][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-06 16:01:49.527][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-06 16:01:49.528][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-06 16:01:49.529][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-06 16:01:49.530][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-06 16:01:49.531][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-06 16:01:49.532][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-06 16:01:49.533][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-06 16:01:49.535][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-06 16:01:49.536][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-06 16:01:49.537][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-06 16:01:49.539][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-06 16:01:49.540][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-06 16:01:49.541][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-06 16:01:49.542][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-06 16:01:49.543][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-06 16:01:49.544][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-06 16:01:49.545][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-06 16:01:49.546][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-06 16:01:49.547][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-06 16:01:49.548][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-06 16:01:49.549][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-06 16:01:49.550][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-06 16:01:49.551][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-06 16:01:49.552][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-06 16:01:49.554][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-06 16:01:49.555][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-06 16:01:49.556][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-06 16:01:49.557][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-06 16:01:49.558][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-06 16:01:49.559][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-06 16:01:49.560][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-06 16:01:49.565][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-06 16:01:49.567][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-06 16:01:49.568][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-06 16:01:49.569][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-06 16:01:49.570][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-06 16:01:49.571][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-06 16:01:49.572][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-06 16:01:49.573][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-06 16:01:49.574][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-06 16:01:49.575][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-06 16:01:49.576][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-06 16:01:49.577][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-06 16:01:49.578][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-06 16:01:49.579][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-06 16:01:49.580][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-06 16:01:49.584][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-06 16:01:49.586][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-09-06 16:01:49.588][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:01:49.589][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.590][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:49.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:49.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:49.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:49.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:49.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:49.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:49.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:49.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:49.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:49.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:49.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:49.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:49.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:49.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:49.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:49.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:49.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:49.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:49.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:49.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:49.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:49.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:49.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:49.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:49.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:49.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:49.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:49.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:49.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:49.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:49.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:49.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:49.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:49.675][bdb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-09-06 16:01:49.682][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-09-06 16:01:49.684][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.684][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-09-06 16:01:49.685][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.686][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:49.687][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.687][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.688][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.689][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.690][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-09-06 16:01:49.691][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:49.692][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.692][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-09-06 16:01:49.693][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:49.694][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-09-06 16:01:49.694][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-09-06 16:01:49.695][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:49.696][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:49.696][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-06 16:01:49.701][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:49.702][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:49.703][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:49.703][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:49.704][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:49.705][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.706][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-09-06 16:01:49.706][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-09-06 16:01:49.706][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:49.707][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:49.708][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.709][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:49.710][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-09-06 16:01:49.711][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.712][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-09-06 16:01:49.713][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.713][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:49.714][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.715][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.716][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.717][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.717][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-06 16:01:49.718][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:49.719][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.720][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-09-06 16:01:49.721][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:49.721][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-09-06 16:01:49.721][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-09-06 16:01:49.721][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-09-06 16:01:49.721][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-09-06 16:01:49.721][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-09-06 16:01:49.721][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-09-06 16:01:49.722][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:49.723][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:01:49.724][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-06 16:01:49.724][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:49.725][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:49.726][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:49.727][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:49.727][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:49.728][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.729][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:49.729][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-09-06 16:01:49.729][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:49.730][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:49.731][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.732][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:49.733][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-09-06 16:01:49.734][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:49.735][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-09-06 16:01:49.736][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.737][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:49.738][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.739][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.739][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.740][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.741][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-06 16:01:49.742][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:49.743][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.744][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-09-06 16:01:49.744][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:49.745][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-09-06 16:01:49.745][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:49.745][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:49.745][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:49.745][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:49.745][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:49.745][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:49.745][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:49.745][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:49.745][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:49.745][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-09-06 16:01:49.745][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:49.745][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:49.745][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:49.746][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:49.747][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:01:49.747][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:01:49.747][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:01:49.748][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-09-06 16:01:49.749][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:49.750][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:49.750][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:49.751][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:49.752][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:49.753][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.754][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:49.754][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-09-06 16:01:49.754][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-09-06 16:01:49.755][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:49.755][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:49.756][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.757][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-09-06 16:01:49.758][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-09-06 16:01:49.760][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.761][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-09-06 16:01:49.762][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.762][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:49.763][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.764][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.765][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.766][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.767][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-06 16:01:49.767][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:49.768][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.769][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-09-06 16:01:49.770][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:49.771][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-09-06 16:01:49.771][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-09-06 16:01:49.772][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:49.772][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:49.773][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-09-06 16:01:49.774][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:49.775][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:49.776][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:49.776][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:49.777][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:49.778][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:49.779][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:49.779][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-09-06 16:01:49.779][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-09-06 16:01:49.780][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:49.780][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:49.781][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:49.782][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-09-06 16:01:49.787][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-09-06 16:01:49.788][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-06 16:01:49.789][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-06 16:01:49.790][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-09-06 16:01:49.792][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-06 16:01:49.793][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-09-06 16:01:49.811][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-09-06 16:01:49.826][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2025-09-06 16:01:49.834][biodb::testThat]
biodb.INFO [2025-09-06 16:01:49.835][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-09-06 16:01:49.835][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:49.836][biodb::testThat]
biodb.TRACE[2025-09-06 16:01:49.840][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2025-09-06 16:01:49.841][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-09-06 16:01:49.843][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-09-06 16:01:49.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-06 16:01:49.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:49.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:49.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:49.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:49.871][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:49.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-06 16:01:49.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:49.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:49.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:49.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:49.899][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-09-06 16:01:49.908][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:49.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:49.910][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:49.930][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-09-06 16:01:49.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:49.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:49.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:49.934][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:49.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:49.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:49.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:49.937][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:49.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:49.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:49.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:49.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:49.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:49.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:49.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:49.943][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:49.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:49.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:49.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:49.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:49.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:49.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:49.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:49.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:49.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:49.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:49.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:49.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:49.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:49.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:49.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:49.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:49.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:49.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:49.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:49.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:49.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:49.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:49.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:49.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:49.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:49.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:49.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:01:49.996][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2025-09-06 16:01:49.998][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:49.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.001][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.022][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:01:50.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:01:50.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.025][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:01:50.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:01:50.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.028][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-06 16:01:50.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-06 16:01:50.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.031][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-06 16:01:50.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-06 16:01:50.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.048][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.077][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.080][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.084][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.107][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.108][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.109][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.122][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-09-06 16:01:50.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.125][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.129][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.133][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-09-06 16:01:50.134][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.135][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.136][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-09-06 16:01:50.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.147][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.148][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.150][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.155][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.156][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.157][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.173][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2025-09-06 16:01:50.234][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-09-06 16:01:50.235][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-09-06 16:01:50.236][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-06 16:01:50.237][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:50.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:50.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:50.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:50.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-06 16:01:50.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.271][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-09-06 16:01:50.272][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.274][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.275][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-09-06 16:01:50.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.278][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.282][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.288][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:01:50.313][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2025-09-06 16:01:50.329][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.333][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.337][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:01:50.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:01:50.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.340][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:01:50.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:01:50.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.350][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-06 16:01:50.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-06 16:01:50.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.353][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-06 16:01:50.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-06 16:01:50.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.366][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.398][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.402][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.405][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:50.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.434][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.435][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.436][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.437][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.448][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-09-06 16:01:50.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.452][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.456][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.459][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-09-06 16:01:50.460][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.462][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.462][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-09-06 16:01:50.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.473][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.474][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:50.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.476][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:50.484][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:50.485][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:50.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:50.487][ef$get] fields variable is a list.
biodb.INFO [2025-09-06 16:01:50.494][biodb::testThat]
biodb.INFO [2025-09-06 16:01:50.495][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-09-06 16:01:50.496][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:50.497][biodb::testThat]
biodb.DEBUG[2025-09-06 16:01:50.499][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2025-09-06 16:01:50.505][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2025-09-06 16:01:50.507][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-09-06 16:01:50.508][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:01:50.509][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-09-06 16:01:50.510][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-06 16:01:50.511][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-09-06 16:01:50.545][biodb::testThat]
biodb.INFO [2025-09-06 16:01:50.546][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-09-06 16:01:50.547][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:50.547][biodb::testThat]
biodb.INFO [2025-09-06 16:01:50.553][biodb::testThat]
biodb.INFO [2025-09-06 16:01:50.554][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-09-06 16:01:50.555][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:50.556][biodb::testThat]
biodb.WARN [2025-09-06 16:01:50.572][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-09-06 16:01:50.587][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-09-06 16:01:50.595][biodb::testThat]
biodb.INFO [2025-09-06 16:01:50.596][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-09-06 16:01:50.597][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:50.598][biodb::testThat]
biodb.DEBUG[2025-09-06 16:01:50.616][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2025-09-06 16:01:50.649][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-09-06 16:01:50.670][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-09-06 16:01:50.672][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:01:50.672][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-09-06 16:01:50.673][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-06 16:01:50.674][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-09-06 16:01:50.707][biodb::testThat]
biodb.INFO [2025-09-06 16:01:50.708][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-09-06 16:01:50.708][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:50.709][biodb::testThat]
biodb.INFO [2025-09-06 16:01:50.721][biodb::testThat]
biodb.INFO [2025-09-06 16:01:50.722][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-09-06 16:01:50.723][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:50.724][biodb::testThat]
biodb.INFO [2025-09-06 16:01:50.730][biodb::testThat]
biodb.INFO [2025-09-06 16:01:50.731][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-09-06 16:01:50.732][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:50.733][biodb::testThat]
biodb.INFO [2025-09-06 16:01:50.744][biodb::testThat]
biodb.INFO [2025-09-06 16:01:50.745][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-09-06 16:01:50.746][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:50.746][biodb::testThat]
biodb.INFO [2025-09-06 16:01:50.752][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-09-06 16:01:50.753][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-09-06 16:01:50.754][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-06 16:01:50.755][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:50.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:50.756][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:50.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:50.757][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-09-06 16:01:50.765][biodb::testContext]
biodb.INFO [2025-09-06 16:01:50.766][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-06 16:01:50.767][biodb::testContext] Test context - Gene long tests
biodb.INFO [2025-09-06 16:01:50.767][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-06 16:01:50.768][biodb::testContext]
biodb.INFO [2025-09-06 16:01:50.770][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-09-06 16:01:50.771][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-09-06 16:01:50.775][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:01:50.775][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-06 16:01:50.776][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-06 16:01:50.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.779][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-06 16:01:50.780][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-06 16:01:50.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.783][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-06 16:01:50.784][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-06 16:01:50.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.787][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-06 16:01:50.792][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-06 16:01:50.793][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-06 16:01:50.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.796][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-06 16:01:50.797][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-06 16:01:50.798][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-06 16:01:50.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.801][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-06 16:01:50.801][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-06 16:01:50.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.804][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-06 16:01:50.805][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-06 16:01:50.806][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-06 16:01:50.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.808][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-06 16:01:50.809][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-06 16:01:50.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.812][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-06 16:01:50.813][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-06 16:01:50.814][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-06 16:01:50.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.817][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-06 16:01:50.817][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-06 16:01:50.818][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-06 16:01:50.819][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-06 16:01:50.820][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-06 16:01:50.821][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-06 16:01:50.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.823][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-06 16:01:50.824][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-06 16:01:50.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.827][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-06 16:01:50.828][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-06 16:01:50.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.831][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-06 16:01:50.832][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-06 16:01:50.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.835][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-06 16:01:50.836][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-06 16:01:50.837][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-06 16:01:50.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.840][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-06 16:01:50.840][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-06 16:01:50.856][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-06 16:01:50.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.860][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-06 16:01:50.860][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-06 16:01:50.861][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-06 16:01:50.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.864][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-06 16:01:50.885][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:50.886][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-09-06 16:01:50.887][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:50.888][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:50.889][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:50.890][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:50.891][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:50.891][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:50.892][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-06 16:01:50.893][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:50.894][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:50.895][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-06 16:01:50.896][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:50.896][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:50.897][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:50.898][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:01:50.898][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:01:50.898][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:01:50.898][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-06 16:01:50.898][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-06 16:01:50.899][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:01:50.900][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:50.900][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:50.901][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:50.902][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:50.907][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:50.908][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:50.908][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:50.909][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:50.910][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:50.911][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:50.912][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:50.913][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-06 16:01:50.914][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:50.915][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-06 16:01:50.916][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:50.917][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:50.917][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:50.918][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:50.919][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:50.920][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:50.921][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-06 16:01:50.921][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:50.922][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:50.923][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-06 16:01:50.924][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:50.925][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:50.925][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:50.926][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:01:50.926][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:01:50.926][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:01:50.926][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-06 16:01:50.926][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-06 16:01:50.927][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:01:50.928][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:50.929][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:50.930][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:50.930][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:50.931][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:50.932][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:50.933][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:50.933][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:50.934][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:50.935][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:50.936][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:50.937][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-06 16:01:50.938][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:50.939][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-09-06 16:01:50.939][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:50.940][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:50.941][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:50.942][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:50.942][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:50.943][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:50.944][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-06 16:01:50.945][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:50.945][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:50.946][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-06 16:01:50.947][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:50.948][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:50.949][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:50.949][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:50.950][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:01:50.951][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:50.952][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:50.953][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:50.953][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:50.954][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:50.955][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:50.956][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:50.956][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:50.957][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:50.958][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:50.959][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:50.959][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-06 16:01:50.961][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:50.961][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-06 16:01:50.962][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:50.963][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:50.964][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:50.965][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:50.966][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:50.966][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:50.967][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-06 16:01:50.968][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:50.969][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:50.970][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-06 16:01:50.971][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:50.971][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:50.972][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:50.973][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:50.974][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:01:50.975][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:50.976][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:50.976][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:50.977][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:50.978][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:50.979][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:50.980][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:50.981][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:50.981][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:50.982][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:50.983][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:50.984][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:01:50.985][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:50.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:50.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:50.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:50.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:50.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:50.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:50.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:50.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:50.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:50.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.064][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-06 16:01:51.065][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-06 16:01:51.067][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-06 16:01:51.069][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-06 16:01:51.070][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-06 16:01:51.072][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-06 16:01:51.073][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-06 16:01:51.075][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-06 16:01:51.077][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-06 16:01:51.080][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-06 16:01:51.082][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-06 16:01:51.084][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-06 16:01:51.085][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-06 16:01:51.086][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-06 16:01:51.088][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-06 16:01:51.090][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-06 16:01:51.092][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-06 16:01:51.094][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-06 16:01:51.096][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-06 16:01:51.098][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-06 16:01:51.100][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-06 16:01:51.101][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-06 16:01:51.103][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-06 16:01:51.105][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-06 16:01:51.106][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-06 16:01:51.107][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-06 16:01:51.109][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-06 16:01:51.110][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-06 16:01:51.111][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-06 16:01:51.112][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-06 16:01:51.113][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-06 16:01:51.115][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-06 16:01:51.116][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-06 16:01:51.117][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-06 16:01:51.118][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-06 16:01:51.119][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-06 16:01:51.121][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-06 16:01:51.122][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-06 16:01:51.123][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-06 16:01:51.124][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-06 16:01:51.125][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-06 16:01:51.127][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-06 16:01:51.128][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-06 16:01:51.129][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-06 16:01:51.130][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-06 16:01:51.131][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-06 16:01:51.132][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-06 16:01:51.134][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-06 16:01:51.135][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-06 16:01:51.136][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-06 16:01:51.138][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-06 16:01:51.139][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-06 16:01:51.140][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-06 16:01:51.141][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-06 16:01:51.143][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-06 16:01:51.144][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-06 16:01:51.145][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-06 16:01:51.146][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-06 16:01:51.148][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-06 16:01:51.153][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-06 16:01:51.154][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-06 16:01:51.155][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-06 16:01:51.156][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-06 16:01:51.158][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-06 16:01:51.159][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-06 16:01:51.160][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-06 16:01:51.161][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-06 16:01:51.162][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-06 16:01:51.163][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-06 16:01:51.164][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-06 16:01:51.165][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-06 16:01:51.166][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-06 16:01:51.168][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-06 16:01:51.169][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-06 16:01:51.170][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-06 16:01:51.171][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-06 16:01:51.172][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-06 16:01:51.173][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-06 16:01:51.174][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-06 16:01:51.175][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-06 16:01:51.176][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-06 16:01:51.178][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-06 16:01:51.179][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-06 16:01:51.180][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-06 16:01:51.181][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-09-06 16:01:51.182][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:01:51.183][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.184][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:51.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:51.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:51.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:51.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:51.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:51.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:51.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:51.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:51.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:51.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:51.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:51.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:51.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:51.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:51.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:51.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:51.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:51.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:51.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:51.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:51.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:51.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:51.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:51.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:51.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:51.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:51.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:51.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:51.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:51.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:51.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:51.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.271][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-09-06 16:01:51.273][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-09-06 16:01:51.274][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.275][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-09-06 16:01:51.276][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.277][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:51.278][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.279][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:51.280][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.280][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:51.281][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-09-06 16:01:51.282][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:51.283][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.284][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-09-06 16:01:51.285][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:51.285][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-09-06 16:01:51.285][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-09-06 16:01:51.286][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:51.287][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:51.288][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-06 16:01:51.289][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:51.289][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:51.290][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:51.291][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:51.291][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:51.292][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:51.293][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-09-06 16:01:51.293][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-09-06 16:01:51.294][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:51.294][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:51.295][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.296][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:51.297][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-09-06 16:01:51.298][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.299][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-09-06 16:01:51.300][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.301][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:51.302][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.303][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:51.304][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.304][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:51.305][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-06 16:01:51.306][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:51.307][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.308][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-09-06 16:01:51.309][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:51.309][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-09-06 16:01:51.309][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-09-06 16:01:51.309][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-09-06 16:01:51.309][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-09-06 16:01:51.309][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-09-06 16:01:51.309][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-09-06 16:01:51.310][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:51.311][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:01:51.312][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-06 16:01:51.313][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:51.314][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:51.314][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:51.315][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:51.316][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:51.317][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:51.317][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:51.317][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-09-06 16:01:51.318][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:51.319][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:51.320][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.320][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:51.322][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-09-06 16:01:51.323][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:51.324][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-09-06 16:01:51.325][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.326][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:51.326][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.327][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:51.328][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.329][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:51.330][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-06 16:01:51.330][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:51.331][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.332][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-09-06 16:01:51.333][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:51.334][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-09-06 16:01:51.334][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:51.334][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:51.334][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:51.334][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:51.334][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:51.334][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:51.334][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:51.334][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:51.334][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:51.334][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-09-06 16:01:51.334][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:51.334][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:51.334][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:51.335][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:51.336][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:01:51.336][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:01:51.336][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:01:51.336][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-09-06 16:01:51.337][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:51.338][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:51.339][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:51.339][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:51.340][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:51.341][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:51.342][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:51.342][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-09-06 16:01:51.342][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-09-06 16:01:51.343][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:51.343][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:51.344][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.345][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-09-06 16:01:51.346][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-09-06 16:01:51.348][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.349][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-09-06 16:01:51.349][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.350][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:51.351][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.352][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:51.352][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.353][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:51.354][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-06 16:01:51.355][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:51.355][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.356][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-09-06 16:01:51.357][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:51.358][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-09-06 16:01:51.358][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-09-06 16:01:51.359][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:51.363][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:51.364][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-09-06 16:01:51.365][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:51.366][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:51.367][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:51.367][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:51.368][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:51.369][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:51.370][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:51.370][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-09-06 16:01:51.370][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-09-06 16:01:51.371][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:51.371][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:51.372][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:51.373][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-09-06 16:01:51.374][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-09-06 16:01:51.375][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-06 16:01:51.376][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-06 16:01:51.378][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-09-06 16:01:51.379][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-06 16:01:51.380][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-09-06 16:01:51.386][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2025-09-06 16:01:51.451][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2025-09-06 16:01:51.460][biodb::testThat]
biodb.INFO [2025-09-06 16:01:51.461][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-09-06 16:01:51.461][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:51.462][biodb::testThat]
biodb.TRACE[2025-09-06 16:01:51.467][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2025-09-06 16:01:51.468][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-09-06 16:01:51.471][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-09-06 16:01:51.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-06 16:01:51.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:51.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:51.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-06 16:01:51.490][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:51.491][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:51.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.493][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:51.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:51.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.497][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:01:51.498][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:01:51.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.500][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.501][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:01:51.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:01:51.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.504][ef$get] Asked field names are: location.
biodb.TRACE[2025-09-06 16:01:51.505][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-09-06 16:01:51.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.506][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.507][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-09-06 16:01:51.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-09-06 16:01:51.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.511][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-09-06 16:01:51.512][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-09-06 16:01:51.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.513][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.514][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-09-06 16:01:51.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-09-06 16:01:51.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.518][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-09-06 16:01:51.518][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:51.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.520][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.521][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-09-06 16:01:51.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:51.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.525][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-09-06 16:01:51.526][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-09-06 16:01:51.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.527][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.529][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-09-06 16:01:51.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-09-06 16:01:51.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.535][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:51.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:51.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.539][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-09-06 16:01:51.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-09-06 16:01:51.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.541][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-09-06 16:01:51.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-09-06 16:01:51.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:51.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:51.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.547][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-09-06 16:01:51.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-09-06 16:01:51.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:51.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:51.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:51.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:51.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:51.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:51.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:51.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:51.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:51.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:51.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:51.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:51.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:01:51.577][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2025-09-06 16:01:51.579][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:51.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:51.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.582][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:51.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:51.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.585][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:51.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:51.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.588][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:51.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:51.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:51.591][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:51.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:51.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:01:51.594][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-09-06 16:01:51.615][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-09-06 16:01:51.626][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2025-09-06 16:01:51.627][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2025-09-06 16:01:51.633][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-09-06 16:01:51.635][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-09-06 16:01:51.636][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:01:51.637][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-09-06 16:01:51.637][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-06 16:01:51.638][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-09-06 16:01:51.651][biodb::testThat]
biodb.INFO [2025-09-06 16:01:51.652][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-09-06 16:01:51.653][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:51.654][biodb::testThat]
biodb.DEBUG[2025-09-06 16:01:51.656][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2025-09-06 16:01:51.657][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2025-09-06 16:01:51.659][cch$loadContents] Load 8 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-09-06 16:01:51.660][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:01:51.661][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:51.662][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-06 16:01:51.663][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-09-06 16:01:51.664][private$retrieveContents] Get entry content(s) for 8 id(s)...
biodb.INFO [2025-09-06 16:01:51.686][biodb::testThat]
biodb.INFO [2025-09-06 16:01:51.687][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-09-06 16:01:51.688][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:51.689][biodb::testThat]
biodb.TRACE[2025-09-06 16:01:51.692][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:01:51.693][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:51.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:51.694][ef$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:01:51.696][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2025-09-06 16:01:51.705][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-09-06 16:01:51.706][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-09-06 16:01:51.708][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-09-06 16:01:51.709][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:01:51.710][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:51.711][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-06 16:01:51.712][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-09-06 16:01:51.726][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-09-06 16:01:51.756][biodb::testThat]
biodb.INFO [2025-09-06 16:01:51.758][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-09-06 16:01:51.759][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:51.761][biodb::testThat]
biodb.DEBUG[2025-09-06 16:01:51.772][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-09-06 16:01:51.773][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-09-06 16:01:51.775][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-09-06 16:01:51.776][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:01:51.777][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:51.783][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-06 16:01:51.784][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-09-06 16:01:51.785][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-09-06 16:01:51.801][biodb::testThat]
biodb.INFO [2025-09-06 16:01:51.802][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-09-06 16:01:51.803][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:51.804][biodb::testThat]
biodb.DEBUG[2025-09-06 16:01:51.808][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-09-06 16:01:51.809][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-09-06 16:01:51.810][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-09-06 16:01:51.811][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:01:51.812][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:51.813][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-06 16:01:51.814][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-09-06 16:01:51.815][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-09-06 16:01:51.831][biodb::testThat]
biodb.INFO [2025-09-06 16:01:51.832][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-09-06 16:01:51.832][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:51.833][biodb::testThat]
biodb.INFO [2025-09-06 16:01:51.850][biodb::testThat]
biodb.INFO [2025-09-06 16:01:51.851][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-09-06 16:01:51.852][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:51.854][biodb::testThat]
biodb.INFO [2025-09-06 16:01:51.864][biodb::testThat]
biodb.INFO [2025-09-06 16:01:51.865][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-09-06 16:01:51.867][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:51.868][biodb::testThat]
biodb.INFO [2025-09-06 16:01:51.886][biodb::testThat]
biodb.INFO [2025-09-06 16:01:51.887][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-09-06 16:01:51.888][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:51.889][biodb::testThat]
biodb.INFO [2025-09-06 16:01:51.895][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-09-06 16:01:51.897][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2025-09-06 16:01:51.898][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-09-06 16:01:51.899][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-06 16:01:51.901][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:51.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:51.903][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:51.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:51.905][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-09-06 16:01:51.913][biodb::testContext]
biodb.INFO [2025-09-06 16:01:51.914][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-06 16:01:51.915][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2025-09-06 16:01:51.916][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-06 16:01:51.916][biodb::testContext]
biodb.INFO [2025-09-06 16:01:51.918][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-09-06 16:01:51.920][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-09-06 16:01:51.923][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:01:51.924][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-06 16:01:51.925][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-06 16:01:51.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.928][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-06 16:01:51.929][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-06 16:01:51.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.932][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-06 16:01:51.933][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-06 16:01:51.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.936][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-06 16:01:51.937][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-06 16:01:51.938][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-06 16:01:51.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.941][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-06 16:01:51.942][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-06 16:01:51.943][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-06 16:01:51.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.946][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-06 16:01:51.947][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-06 16:01:51.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.950][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-06 16:01:51.950][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-06 16:01:51.951][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-06 16:01:51.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.954][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-06 16:01:51.955][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-06 16:01:51.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.958][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-06 16:01:51.959][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-06 16:01:51.960][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-06 16:01:51.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.963][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-06 16:01:51.963][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-06 16:01:51.964][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-06 16:01:51.965][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-06 16:01:51.966][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-06 16:01:51.967][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-06 16:01:51.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.970][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-06 16:01:51.971][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-06 16:01:51.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.974][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-06 16:01:51.974][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-06 16:01:51.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.977][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-06 16:01:51.978][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-06 16:01:51.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.981][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-06 16:01:51.982][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-06 16:01:51.983][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-06 16:01:51.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:51.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:51.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:51.985][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-06 16:01:51.986][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-06 16:01:52.003][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-06 16:01:52.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.006][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-06 16:01:52.007][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-06 16:01:52.008][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-06 16:01:52.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.011][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-06 16:01:52.012][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:52.013][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-09-06 16:01:52.014][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.015][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:52.016][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.016][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.017][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:52.018][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.019][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-06 16:01:52.019][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:52.020][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.021][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-06 16:01:52.022][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:52.027][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:52.028][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.028][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:01:52.028][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:01:52.028][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:01:52.028][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-06 16:01:52.028][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-06 16:01:52.029][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:01:52.030][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:52.031][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:52.032][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:52.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:52.033][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:52.034][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.035][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:52.036][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:52.036][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:52.037][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:52.038][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:52.039][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-06 16:01:52.040][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:52.041][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-06 16:01:52.042][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.043][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:52.043][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.044][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.045][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:52.046][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.047][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-06 16:01:52.048][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:52.048][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.049][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-06 16:01:52.050][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:52.051][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:52.051][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.052][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:01:52.052][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:01:52.052][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:01:52.052][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-06 16:01:52.052][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-06 16:01:52.053][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:01:52.054][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:52.055][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:52.055][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:52.056][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:52.057][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:52.058][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.058][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:52.059][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:52.060][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:52.061][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:52.061][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:52.062][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-06 16:01:52.064][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.065][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-09-06 16:01:52.066][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.066][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:52.067][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.068][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.069][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:52.070][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.070][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-06 16:01:52.071][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:52.072][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:52.073][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-06 16:01:52.074][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:52.075][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:52.075][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.076][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:52.077][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:01:52.078][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:52.079][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:52.079][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:52.080][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:52.081][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:52.081][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.082][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:52.085][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:52.086][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:52.087][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:52.088][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:52.090][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-06 16:01:52.100][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.102][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-06 16:01:52.105][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.106][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:52.107][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.110][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.110][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:52.111][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.112][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-06 16:01:52.113][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:52.113][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:52.114][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-06 16:01:52.115][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:52.116][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:52.117][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.117][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:52.118][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:01:52.119][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:52.119][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:52.120][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:52.121][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:52.122][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:52.123][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.123][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:52.124][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:52.125][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:52.126][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:52.126][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:52.127][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:01:52.128][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.188][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-06 16:01:52.189][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-06 16:01:52.190][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-06 16:01:52.191][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-06 16:01:52.193][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-06 16:01:52.194][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-06 16:01:52.195][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-06 16:01:52.196][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-06 16:01:52.197][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-06 16:01:52.198][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-06 16:01:52.199][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-06 16:01:52.200][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-06 16:01:52.201][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-06 16:01:52.202][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-06 16:01:52.203][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-06 16:01:52.204][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-06 16:01:52.205][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-06 16:01:52.207][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-06 16:01:52.208][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-06 16:01:52.209][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-06 16:01:52.210][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-06 16:01:52.211][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-06 16:01:52.212][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-06 16:01:52.213][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-06 16:01:52.214][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-06 16:01:52.215][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-06 16:01:52.216][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-06 16:01:52.218][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-06 16:01:52.219][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-06 16:01:52.220][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-06 16:01:52.221][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-06 16:01:52.222][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-06 16:01:52.227][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-06 16:01:52.229][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-06 16:01:52.230][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-06 16:01:52.231][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-06 16:01:52.232][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-06 16:01:52.233][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-06 16:01:52.234][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-06 16:01:52.235][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-06 16:01:52.236][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-06 16:01:52.238][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-06 16:01:52.239][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-06 16:01:52.240][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-06 16:01:52.241][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-06 16:01:52.242][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-06 16:01:52.243][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-06 16:01:52.244][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-06 16:01:52.245][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-06 16:01:52.246][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-06 16:01:52.247][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-06 16:01:52.249][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-06 16:01:52.250][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-06 16:01:52.251][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-06 16:01:52.252][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-06 16:01:52.253][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-06 16:01:52.254][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-06 16:01:52.255][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-06 16:01:52.256][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-06 16:01:52.257][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-06 16:01:52.258][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-06 16:01:52.259][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-06 16:01:52.261][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-06 16:01:52.262][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-06 16:01:52.263][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-06 16:01:52.264][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-06 16:01:52.265][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-06 16:01:52.266][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-06 16:01:52.267][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-06 16:01:52.268][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-06 16:01:52.269][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-06 16:01:52.270][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-06 16:01:52.272][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-06 16:01:52.273][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-06 16:01:52.274][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-06 16:01:52.275][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-06 16:01:52.276][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-06 16:01:52.277][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-06 16:01:52.278][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-06 16:01:52.279][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-06 16:01:52.280][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-06 16:01:52.281][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-06 16:01:52.282][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-06 16:01:52.283][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-06 16:01:52.285][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-09-06 16:01:52.286][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:01:52.286][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.288][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:52.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:52.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:52.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:52.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:52.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:52.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:52.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:52.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:52.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:52.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:52.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:52.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:52.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:52.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:52.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:52.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:52.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:52.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:52.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:52.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:52.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:52.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:52.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:52.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:52.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:52.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:52.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:52.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:52.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:52.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:52.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:52.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:52.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:52.375][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-09-06 16:01:52.377][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-09-06 16:01:52.378][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.379][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-09-06 16:01:52.380][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.381][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:52.381][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.382][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.383][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.384][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.384][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-09-06 16:01:52.385][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:52.386][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.387][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-09-06 16:01:52.387][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:52.388][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-09-06 16:01:52.388][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-09-06 16:01:52.389][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:52.390][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:52.391][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-06 16:01:52.392][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:52.392][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:52.393][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:52.394][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:52.395][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:52.396][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.396][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-09-06 16:01:52.396][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-09-06 16:01:52.397][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:52.398][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:52.399][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.400][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:52.401][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-09-06 16:01:52.402][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.403][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-09-06 16:01:52.404][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.405][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:52.405][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.406][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.407][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.412][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.413][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-06 16:01:52.414][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:52.414][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.415][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-09-06 16:01:52.416][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:52.417][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-09-06 16:01:52.417][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-09-06 16:01:52.417][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-09-06 16:01:52.417][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-09-06 16:01:52.417][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-09-06 16:01:52.417][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-09-06 16:01:52.418][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:52.419][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:01:52.419][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-06 16:01:52.420][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:52.421][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:52.422][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:52.423][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:52.423][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:52.424][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.425][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:52.425][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-09-06 16:01:52.426][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:52.426][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:52.427][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.428][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:52.429][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-09-06 16:01:52.431][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:52.431][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-09-06 16:01:52.432][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.433][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:52.434][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.434][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.435][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.436][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.437][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-06 16:01:52.438][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:52.438][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.439][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-09-06 16:01:52.440][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:52.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-09-06 16:01:52.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:52.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:52.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:52.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:52.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:52.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:52.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:52.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:52.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:52.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-09-06 16:01:52.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:52.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:52.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:52.442][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:52.442][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:01:52.442][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:01:52.442][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:01:52.443][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-09-06 16:01:52.444][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:52.444][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:52.445][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:52.446][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:52.447][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:52.447][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.448][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:52.448][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-09-06 16:01:52.448][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-09-06 16:01:52.449][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:52.449][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:52.450][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.451][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-09-06 16:01:52.452][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-09-06 16:01:52.453][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.454][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-09-06 16:01:52.455][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.456][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:52.457][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.457][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.458][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.459][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.460][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-06 16:01:52.460][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:52.461][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.462][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-09-06 16:01:52.463][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:52.464][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-09-06 16:01:52.464][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-09-06 16:01:52.464][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:52.465][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:52.466][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-09-06 16:01:52.467][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:52.467][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:52.468][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:52.469][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:52.470][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:52.471][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:52.471][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:52.471][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-09-06 16:01:52.471][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-09-06 16:01:52.472][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:52.473][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:52.474][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:52.474][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-09-06 16:01:52.475][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-09-06 16:01:52.477][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-06 16:01:52.478][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-06 16:01:52.479][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-09-06 16:01:52.480][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-06 16:01:52.481][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-09-06 16:01:52.487][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2025-09-06 16:01:52.496][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2025-09-06 16:01:52.500][biodb::testThat]
biodb.INFO [2025-09-06 16:01:52.500][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-09-06 16:01:52.501][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:52.502][biodb::testThat]
biodb.TRACE[2025-09-06 16:01:52.504][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2025-09-06 16:01:52.521][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-09-06 16:01:52.525][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-09-06 16:01:52.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-06 16:01:52.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:52.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:52.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:52.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:52.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:52.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-06 16:01:52.538][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.539][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.541][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.545][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.546][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.547][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.548][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.552][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:52.552][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:52.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.554][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.555][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:52.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:52.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.560][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:52.561][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:52.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.562][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.563][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:52.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:52.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.567][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:52.568][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:52.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.569][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.570][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:52.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:52.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.574][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:52.575][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:52.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.576][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.578][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:52.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:52.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.581][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-09-06 16:01:52.582][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:52.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.583][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.584][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-09-06 16:01:52.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:52.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.587][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:01:52.588][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:01:52.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.590][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.591][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:01:52.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:01:52.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.594][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:01:52.595][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:01:52.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.596][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.597][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:01:52.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:01:52.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.600][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:01:52.601][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:01:52.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.602][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.603][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:01:52.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:01:52.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.606][ef$get] Asked field names are: logp.
biodb.TRACE[2025-09-06 16:01:52.607][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-09-06 16:01:52.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.609][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.610][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-09-06 16:01:52.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-09-06 16:01:52.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.613][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-09-06 16:01:52.614][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:52.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.620][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-09-06 16:01:52.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:52.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.625][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:52.626][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:52.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.627][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.628][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:52.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:52.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.631][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:52.632][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:52.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.634][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.635][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:52.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:52.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.638][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-09-06 16:01:52.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:52.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.641][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:52.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:52.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.645][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:52.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:52.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.648][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-09-06 16:01:52.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.651][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.654][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.658][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-09-06 16:01:52.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:52.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.660][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:52.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:52.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.664][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:52.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:52.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.667][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-09-06 16:01:52.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:52.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.670][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:52.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:52.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.673][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:52.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:52.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.676][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-09-06 16:01:52.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:52.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.679][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:52.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:52.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.682][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:52.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:52.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.685][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:01:52.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:52.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.688][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:52.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:52.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.691][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:52.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:52.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.697][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:52.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:52.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:01:52.724][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2025-09-06 16:01:52.726][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:52.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:52.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.729][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:52.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:52.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.732][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:52.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:52.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.735][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:01:52.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:01:52.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.738][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:01:52.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:01:52.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.741][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-06 16:01:52.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-06 16:01:52.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.744][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-06 16:01:52.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-06 16:01:52.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.756][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:52.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:52.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.783][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:52.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:52.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.786][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:52.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:52.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.789][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:52.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:52.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.811][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.812][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.814][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:52.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:52.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.825][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-09-06 16:01:52.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:52.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:52.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:52.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:52.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:52.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.835][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-09-06 16:01:52.836][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:52.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.837][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.838][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-09-06 16:01:52.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:52.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-09-06 16:01:52.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:52.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:52.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:52.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:52.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:52.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.857][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-09-06 16:01:52.858][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:52.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.859][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-09-06 16:01:52.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:52.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.870][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:01:52.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:01:52.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.873][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:01:52.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:01:52.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.876][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:01:52.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:01:52.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.880][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:01:52.880][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:01:52.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.882][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.883][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:01:52.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:01:52.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.897][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-09-06 16:01:52.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-09-06 16:01:52.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.900][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-09-06 16:01:52.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-09-06 16:01:52.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.903][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-09-06 16:01:52.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-09-06 16:01:52.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.906][ef$get] Asked field names are: logp.
biodb.TRACE[2025-09-06 16:01:52.907][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-09-06 16:01:52.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.909][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.909][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-09-06 16:01:52.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-09-06 16:01:52.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.920][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:52.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:52.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.923][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:52.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:52.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.926][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:52.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:52.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.929][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:52.930][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:52.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.931][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.932][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:52.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:52.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.942][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:52.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:52.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.945][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:52.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:52.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.948][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:52.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:52.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.951][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:52.952][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:52.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.953][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.954][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:52.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:52.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.964][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.968][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.971][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.974][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.975][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.977][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.978][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:52.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.992][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:52.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:52.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.996][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:52.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:52.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:52.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:52.998][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:52.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.002][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.003][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.004][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.005][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.015][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.019][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.022][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.025][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.026][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.028][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.029][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.039][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.042][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.045][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.048][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.049][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.050][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.051][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.061][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.065][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.068][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.072][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.073][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.074][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.075][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.089][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:01:53.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:53.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.093][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:01:53.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:53.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.096][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:01:53.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:53.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.099][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:01:53.100][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:53.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.101][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:01:53.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:53.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.112][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.116][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.119][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.122][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.123][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.124][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.125][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.135][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:01:53.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:01:53.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.138][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:01:53.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:01:53.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.141][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:01:53.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:01:53.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.144][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:01:53.145][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:01:53.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.147][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.148][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:01:53.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:01:53.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.158][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.159][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.161][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.165][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.166][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.168][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.172][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.173][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.175][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.184][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.185][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.186][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.191][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.192][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.193][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.197][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.198][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.200][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.204][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:01:53.205][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:01:53.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.207][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.211][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:01:53.212][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:01:53.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.214][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.218][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.219][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.221][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.225][ef$get] Asked field names are: logp.
biodb.TRACE[2025-09-06 16:01:53.226][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-09-06 16:01:53.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.228][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.232][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:53.233][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:53.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.235][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.239][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:53.240][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:53.241][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.241][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.246][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:01:53.246][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:53.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.248][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.252][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:53.253][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:53.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.255][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.259][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:53.260][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:53.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.261][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.266][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2025-09-06 16:01:53.267][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-09-06 16:01:53.268][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-09-06 16:01:53.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-06 16:01:53.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:53.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:53.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:53.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:53.278][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:53.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-06 16:01:53.280][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.286][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.287][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.303][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.304][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.306][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.307][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.310][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.311][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.312][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.314][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.317][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.318][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.318][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.319][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.320][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.324][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.325][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.327][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.328][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.331][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.332][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.333][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.335][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.338][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-09-06 16:01:53.339][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:53.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.341][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.342][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-09-06 16:01:53.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:53.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.345][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:01:53.346][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:01:53.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.347][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.348][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:01:53.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:01:53.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.351][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:01:53.352][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:01:53.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.354][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.355][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:01:53.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:01:53.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.359][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.360][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.361][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.366][ef$get] Asked field names are: logp.
biodb.TRACE[2025-09-06 16:01:53.366][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-09-06 16:01:53.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.368][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.373][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-09-06 16:01:53.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-09-06 16:01:53.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.377][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-09-06 16:01:53.378][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:53.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.379][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-09-06 16:01:53.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:53.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.384][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:53.385][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:53.385][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.386][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.387][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:53.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:53.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.390][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:53.391][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:53.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.392][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.394][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:53.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:53.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.397][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-09-06 16:01:53.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.401][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.404][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.407][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-09-06 16:01:53.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.410][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.414][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.417][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-09-06 16:01:53.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.420][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.423][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.426][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-09-06 16:01:53.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.430][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.433][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.436][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-09-06 16:01:53.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.440][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.443][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.447][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:01:53.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:53.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.450][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:53.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:53.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.454][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:53.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:53.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.460][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:53.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:53.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:01:53.488][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2025-09-06 16:01:53.490][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:53.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:53.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.493][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:53.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:53.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.496][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:53.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:53.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.499][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:01:53.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:01:53.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.502][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:01:53.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:01:53.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.505][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-06 16:01:53.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-06 16:01:53.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.508][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-06 16:01:53.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-06 16:01:53.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.520][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:53.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:53.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.549][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:53.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:53.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.552][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:53.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:53.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.559][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:53.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:53.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.579][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.580][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.581][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.593][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:53.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:53.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:53.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:53.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:53.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:53.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.602][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:53.603][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:53.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.605][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:53.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:53.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:53.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:53.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:53.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:53.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:53.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:53.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.626][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:53.627][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:53.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.628][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:53.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:53.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.640][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:01:53.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:01:53.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.643][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:01:53.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:01:53.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.646][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:01:53.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:01:53.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.650][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:01:53.650][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:01:53.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.652][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.657][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:01:53.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:01:53.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.668][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-09-06 16:01:53.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-09-06 16:01:53.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.672][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-09-06 16:01:53.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-09-06 16:01:53.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.675][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-09-06 16:01:53.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-09-06 16:01:53.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.678][ef$get] Asked field names are: logp.
biodb.TRACE[2025-09-06 16:01:53.678][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-09-06 16:01:53.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.680][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.681][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-09-06 16:01:53.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-09-06 16:01:53.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.691][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:53.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:53.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.695][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:53.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:53.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.698][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:53.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:53.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.701][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:53.702][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:53.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.703][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.704][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:53.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:53.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.715][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:53.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:53.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.718][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:53.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:53.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.722][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:53.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:53.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.725][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:53.725][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:53.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.727][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.728][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:53.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:53.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.739][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.742][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.746][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.749][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.754][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.756][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:01:53.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.767][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:01:53.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:01:53.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.771][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:01:53.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:01:53.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:01:53.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:01:53.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.777][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:01:53.778][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:01:53.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.779][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.780][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:01:53.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:01:53.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.790][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.793][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.797][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.800][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.801][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.803][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.804][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.814][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.818][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.821][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.825][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.825][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.827][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.828][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.838][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.841][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.844][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.852][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.853][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.855][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.856][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.866][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.870][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.873][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.876][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.877][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.879][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.880][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.890][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.894][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.897][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.901][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.902][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.903][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.904][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.915][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:01:53.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:53.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:01:53.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:53.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.921][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:01:53.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:53.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.925][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:01:53.926][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:53.926][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.927][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.928][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:01:53.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:53.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.939][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:53.940][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:53.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.941][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.951][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.951][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-09-06 16:01:53.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.953][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.958][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.958][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-09-06 16:01:53.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.960][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.965][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.966][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-09-06 16:01:53.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.967][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.972][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.973][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:01:53.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.974][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.979][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.980][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:01:53.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.981][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.986][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:01:53.987][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:01:53.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.988][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:53.993][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:01:53.994][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:01:53.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:53.995][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:54.000][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:01:54.001][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:01:54.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:54.003][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:54.007][ef$get] Asked field names are: logp.
biodb.TRACE[2025-09-06 16:01:54.008][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-09-06 16:01:54.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:54.010][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:54.014][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:54.015][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:54.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:54.017][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:54.022][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:54.022][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:01:54.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:54.024][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:54.029][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:01:54.030][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:54.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:54.031][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:54.036][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:54.037][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-09-06 16:01:54.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:54.038][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:54.043][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:54.044][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-09-06 16:01:54.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:54.046][ef$get] fields variable is a list.
biodb.INFO [2025-09-06 16:01:54.058][biodb::testThat]
biodb.INFO [2025-09-06 16:01:54.059][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-09-06 16:01:54.060][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:54.061][biodb::testThat]
biodb.DEBUG[2025-09-06 16:01:54.063][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-09-06 16:01:54.069][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-09-06 16:01:54.071][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
fscache.DEBUG[2025-09-06 16:01:54.076][FUN] Found encoding ISO-8859-1 for file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/65124.xml.
biodb.DEBUG[2025-09-06 16:01:54.077][conn$getEntryContent] 1 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:01:54.078][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:54.079][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-06 16:01:54.080][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-09-06 16:01:54.081][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-09-06 16:01:54.093][biodb::testThat]
biodb.INFO [2025-09-06 16:01:54.094][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-09-06 16:01:54.094][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:54.095][biodb::testThat]
biodb.TRACE[2025-09-06 16:01:54.098][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:01:54.099][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:54.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:54.100][ef$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:01:54.102][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2025-09-06 16:01:54.110][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-09-06 16:01:54.111][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-09-06 16:01:54.112][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-09-06 16:01:54.113][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:01:54.114][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:54.115][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-06 16:01:54.116][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-09-06 16:01:54.117][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-09-06 16:01:54.128][biodb::testThat]
biodb.INFO [2025-09-06 16:01:54.129][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-09-06 16:01:54.130][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:54.131][biodb::testThat]
biodb.DEBUG[2025-09-06 16:01:54.138][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-09-06 16:01:54.139][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-09-06 16:01:54.140][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-09-06 16:01:54.141][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:01:54.142][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:54.142][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-06 16:01:54.143][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-09-06 16:01:54.144][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-09-06 16:01:54.156][biodb::testThat]
biodb.INFO [2025-09-06 16:01:54.157][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-09-06 16:01:54.158][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:54.159][biodb::testThat]
biodb.DEBUG[2025-09-06 16:01:54.167][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-09-06 16:01:54.168][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-09-06 16:01:54.169][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-09-06 16:01:54.170][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:01:54.171][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:54.172][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-06 16:01:54.173][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-09-06 16:01:54.173][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-09-06 16:01:54.186][biodb::testThat]
biodb.INFO [2025-09-06 16:01:54.186][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-09-06 16:01:54.187][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:54.188][biodb::testThat]
biodb.INFO [2025-09-06 16:01:54.201][biodb::testThat]
biodb.INFO [2025-09-06 16:01:54.202][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-09-06 16:01:54.203][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:54.203][biodb::testThat]
biodb.INFO [2025-09-06 16:01:54.217][biodb::testThat]
biodb.INFO [2025-09-06 16:01:54.217][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-09-06 16:01:54.218][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:54.219][biodb::testThat]
biodb.INFO [2025-09-06 16:01:54.231][biodb::testThat]
biodb.INFO [2025-09-06 16:01:54.232][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-09-06 16:01:54.233][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:54.234][biodb::testThat]
biodb.TRACE[2025-09-06 16:01:54.252][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:01:54.253][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:54.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:54.260][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:54.260][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:54.261][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:54.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:54.263][ef$get] fields variable is a list.
biodb.INFO [2025-09-06 16:01:54.264][biodb::testThat]
biodb.INFO [2025-09-06 16:01:54.265][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-09-06 16:01:54.266][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:54.267][biodb::testThat]
biodb.DEBUG[2025-09-06 16:01:54.274][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-09-06 16:01:54.274][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-09-06 16:01:54.276][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-09-06 16:01:54.277][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:01:54.278][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:54.278][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-06 16:01:54.279][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-09-06 16:01:54.280][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-09-06 16:01:54.292][biodb::testThat]
biodb.INFO [2025-09-06 16:01:54.293][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-09-06 16:01:54.294][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:54.294][biodb::testThat]
biodb.DEBUG[2025-09-06 16:01:54.297][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-09-06 16:01:54.298][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-09-06 16:01:54.299][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
fscache.DEBUG[2025-09-06 16:01:54.303][FUN] Found encoding ISO-8859-1 for file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/65124.xml.
biodb.DEBUG[2025-09-06 16:01:54.304][conn$getEntryContent] 1 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:01:54.305][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:54.306][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-06 16:01:54.306][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-09-06 16:01:54.307][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-09-06 16:01:54.319][biodb::testThat]
biodb.INFO [2025-09-06 16:01:54.320][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-09-06 16:01:54.321][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:54.322][biodb::testThat]
biodb.DEBUG[2025-09-06 16:01:54.324][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-09-06 16:01:54.325][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-09-06 16:01:54.326][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
fscache.DEBUG[2025-09-06 16:01:54.330][FUN] Found encoding ISO-8859-1 for file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/65124.xml.
biodb.DEBUG[2025-09-06 16:01:54.331][conn$getEntryContent] 1 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:01:54.331][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:54.332][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-06 16:01:54.333][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-09-06 16:01:54.334][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-09-06 16:01:54.346][biodb::testThat]
biodb.INFO [2025-09-06 16:01:54.347][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-09-06 16:01:54.348][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:54.348][biodb::testThat]
biodb.DEBUG[2025-09-06 16:01:54.351][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-09-06 16:01:54.352][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-09-06 16:01:54.353][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
fscache.DEBUG[2025-09-06 16:01:54.361][FUN] Found encoding ISO-8859-1 for file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/65124.xml.
biodb.DEBUG[2025-09-06 16:01:54.362][conn$getEntryContent] 1 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:01:54.363][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:54.364][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-06 16:01:54.365][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-09-06 16:01:54.366][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-06 16:01:54.377][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:01:54.378][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:01:54.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:54.379][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:54.380][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:54.381][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:01:54.382][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:54.383][ef$get] fields variable is a list.
biodb.INFO [2025-09-06 16:01:54.384][biodb::testThat]
biodb.INFO [2025-09-06 16:01:54.385][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2025-09-06 16:01:54.385][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:54.386][biodb::testThat]
biodb.DEBUG[2025-09-06 16:01:54.389][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-09-06 16:01:54.390][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-09-06 16:01:54.391][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
fscache.DEBUG[2025-09-06 16:01:54.394][FUN] Found encoding ISO-8859-1 for file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/65124.xml.
biodb.DEBUG[2025-09-06 16:01:54.395][conn$getEntryContent] 1 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:01:54.396][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:54.397][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-06 16:01:54.398][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-09-06 16:01:54.399][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-09-06 16:01:54.411][biodb::testThat]
biodb.INFO [2025-09-06 16:01:54.412][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2025-09-06 16:01:54.413][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:54.414][biodb::testThat]
biodb.DEBUG[2025-09-06 16:01:54.416][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-09-06 16:01:54.417][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-09-06 16:01:54.418][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
fscache.DEBUG[2025-09-06 16:01:54.422][FUN] Found encoding ISO-8859-1 for file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/65124.xml.
biodb.DEBUG[2025-09-06 16:01:54.423][conn$getEntryContent] 1 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:01:54.424][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:54.424][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-09-06 16:01:54.425][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-09-06 16:01:54.426][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-09-06 16:01:54.437][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-09-06 16:01:54.438][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2025-09-06 16:01:54.439][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-06 16:01:54.440][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:54.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:54.441][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.443][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-09-06 16:01:54.447][biodb::testContext]
biodb.INFO [2025-09-06 16:01:54.448][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-06 16:01:54.449][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2025-09-06 16:01:54.450][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-06 16:01:54.450][biodb::testContext]
biodb.INFO [2025-09-06 16:01:54.452][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-09-06 16:01:54.454][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-09-06 16:01:54.462][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:01:54.463][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-06 16:01:54.464][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-06 16:01:54.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.467][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-06 16:01:54.468][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-06 16:01:54.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.471][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-06 16:01:54.471][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-06 16:01:54.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.474][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-06 16:01:54.475][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-06 16:01:54.476][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-06 16:01:54.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.479][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-06 16:01:54.480][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-06 16:01:54.481][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-06 16:01:54.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.484][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-06 16:01:54.484][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-06 16:01:54.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.487][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-06 16:01:54.488][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-06 16:01:54.489][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-06 16:01:54.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.492][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-06 16:01:54.493][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-06 16:01:54.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.495][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-06 16:01:54.496][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-06 16:01:54.497][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-06 16:01:54.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.500][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-06 16:01:54.501][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-06 16:01:54.502][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-06 16:01:54.502][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-06 16:01:54.503][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-06 16:01:54.504][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-06 16:01:54.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.507][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-06 16:01:54.508][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-06 16:01:54.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.511][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-06 16:01:54.512][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-06 16:01:54.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.515][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-06 16:01:54.516][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-06 16:01:54.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.519][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-06 16:01:54.520][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-06 16:01:54.521][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-06 16:01:54.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.524][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-06 16:01:54.525][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-06 16:01:54.544][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-06 16:01:54.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.547][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-06 16:01:54.548][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-06 16:01:54.549][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-06 16:01:54.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.552][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-06 16:01:54.584][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:54.585][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-09-06 16:01:54.586][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.587][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:54.588][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.589][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.590][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:54.591][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.591][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-06 16:01:54.592][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:54.593][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.594][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-06 16:01:54.595][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:54.596][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:54.596][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.597][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:01:54.597][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:01:54.597][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:01:54.597][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-06 16:01:54.597][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-06 16:01:54.598][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:01:54.599][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:54.600][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:54.601][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:54.601][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:54.602][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:54.603][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.604][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:54.605][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:54.605][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:54.606][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:54.607][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:54.608][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-06 16:01:54.610][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:54.611][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-06 16:01:54.612][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.612][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:54.613][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.614][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.615][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:54.616][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.617][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-06 16:01:54.618][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:54.618][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.619][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-06 16:01:54.620][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:54.621][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:54.622][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.623][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:01:54.623][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:01:54.623][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:01:54.623][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-06 16:01:54.623][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-06 16:01:54.624][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:01:54.624][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:54.625][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:54.626][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:54.627][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:54.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:54.628][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.629][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:54.630][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:54.631][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:54.631][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:54.632][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:54.633][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-06 16:01:54.635][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.636][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-09-06 16:01:54.636][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.637][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:54.638][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.639][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.640][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:54.641][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.641][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-06 16:01:54.642][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:54.643][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:54.644][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-06 16:01:54.645][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:54.646][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:54.646][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.647][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:54.648][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:01:54.649][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:54.650][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:54.650][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:54.651][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:54.652][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:54.657][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.658][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:54.659][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:54.660][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:54.661][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:54.661][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:54.662][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-06 16:01:54.664][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.665][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-06 16:01:54.666][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.666][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:54.667][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.668][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.669][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:54.670][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.671][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-06 16:01:54.671][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:54.672][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:54.673][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-06 16:01:54.674][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:54.674][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:54.675][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.676][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:54.677][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:01:54.677][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:54.678][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:54.679][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:54.680][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:54.680][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:54.681][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.682][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:54.683][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:54.684][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:54.684][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:54.685][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:54.686][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:01:54.687][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.751][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-06 16:01:54.752][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-06 16:01:54.753][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-06 16:01:54.754][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-06 16:01:54.755][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-06 16:01:54.757][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-06 16:01:54.758][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-06 16:01:54.759][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-06 16:01:54.760][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-06 16:01:54.761][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-06 16:01:54.762][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-06 16:01:54.763][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-06 16:01:54.764][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-06 16:01:54.765][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-06 16:01:54.767][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-06 16:01:54.768][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-06 16:01:54.769][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-06 16:01:54.770][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-06 16:01:54.771][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-06 16:01:54.772][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-06 16:01:54.773][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-06 16:01:54.774][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-06 16:01:54.776][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-06 16:01:54.777][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-06 16:01:54.778][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-06 16:01:54.779][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-06 16:01:54.780][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-06 16:01:54.781][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-06 16:01:54.782][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-06 16:01:54.783][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-06 16:01:54.785][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-06 16:01:54.786][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-06 16:01:54.787][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-06 16:01:54.788][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-06 16:01:54.789][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-06 16:01:54.790][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-06 16:01:54.791][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-06 16:01:54.792][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-06 16:01:54.793][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-06 16:01:54.795][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-06 16:01:54.796][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-06 16:01:54.797][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-06 16:01:54.798][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-06 16:01:54.799][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-06 16:01:54.800][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-06 16:01:54.801][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-06 16:01:54.802][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-06 16:01:54.803][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-06 16:01:54.804][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-06 16:01:54.805][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-06 16:01:54.806][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-06 16:01:54.808][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-06 16:01:54.809][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-06 16:01:54.810][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-06 16:01:54.811][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-06 16:01:54.812][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-06 16:01:54.813][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-06 16:01:54.814][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-06 16:01:54.815][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-06 16:01:54.816][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-06 16:01:54.817][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-06 16:01:54.819][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-06 16:01:54.820][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-06 16:01:54.821][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-06 16:01:54.823][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-06 16:01:54.824][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-06 16:01:54.829][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-06 16:01:54.831][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-06 16:01:54.832][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-06 16:01:54.833][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-06 16:01:54.834][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-06 16:01:54.835][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-06 16:01:54.837][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-06 16:01:54.838][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-06 16:01:54.839][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-06 16:01:54.840][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-06 16:01:54.841][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-06 16:01:54.842][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-06 16:01:54.844][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-06 16:01:54.845][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-06 16:01:54.846][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-06 16:01:54.847][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-06 16:01:54.848][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-06 16:01:54.849][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-06 16:01:54.851][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-09-06 16:01:54.851][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:01:54.852][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.854][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:54.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:54.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:54.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:54.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:54.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:54.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:54.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:54.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:54.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:54.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:54.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:54.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:54.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:54.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:54.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:54.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:54.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:54.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:54.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:54.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:54.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:54.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:54.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:54.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:54.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:54.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:54.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:54.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:54.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:54.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:01:54.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:54.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:54.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:54.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:54.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:54.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:01:54.943][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-09-06 16:01:54.945][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-09-06 16:01:54.946][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.947][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-09-06 16:01:54.948][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.949][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:54.949][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.950][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.951][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.952][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.953][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-09-06 16:01:54.953][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:54.954][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.955][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-09-06 16:01:54.956][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:54.957][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-09-06 16:01:54.957][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-09-06 16:01:54.958][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:54.958][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:54.959][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-06 16:01:54.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:54.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:54.962][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:54.962][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:54.963][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:54.964][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.965][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-09-06 16:01:54.965][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-09-06 16:01:54.965][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:54.966][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:54.967][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.968][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:54.969][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-09-06 16:01:54.970][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.971][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-09-06 16:01:54.972][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.972][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:54.973][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.974][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.975][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.975][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.976][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-06 16:01:54.977][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:54.978][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.979][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-09-06 16:01:54.979][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:54.980][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-09-06 16:01:54.980][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-09-06 16:01:54.980][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-09-06 16:01:54.980][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-09-06 16:01:54.980][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-09-06 16:01:54.980][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-09-06 16:01:54.981][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:54.982][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:01:54.983][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-06 16:01:54.984][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:54.984][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:54.985][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:54.986][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:54.987][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:54.988][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.988][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:54.988][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-09-06 16:01:54.989][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:54.990][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:54.991][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.992][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:54.993][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-09-06 16:01:54.994][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:54.995][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-09-06 16:01:54.996][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.997][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:54.997][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:54.998][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:54.999][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:55.004][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:55.005][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-06 16:01:55.006][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:55.007][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:55.008][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-09-06 16:01:55.009][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:55.010][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-09-06 16:01:55.010][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:55.010][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:55.010][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:55.010][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:55.010][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:55.010][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:55.010][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:55.010][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:55.010][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:55.010][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-09-06 16:01:55.010][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:55.010][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:55.010][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-09-06 16:01:55.011][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:55.012][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:01:55.012][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:01:55.012][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:01:55.013][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-09-06 16:01:55.013][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:55.014][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:55.015][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:55.016][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:55.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:55.017][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:55.018][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:55.018][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-09-06 16:01:55.018][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-09-06 16:01:55.019][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:55.020][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:55.021][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:55.021][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-09-06 16:01:55.023][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-09-06 16:01:55.024][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:55.025][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-09-06 16:01:55.026][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:55.027][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:01:55.027][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:55.028][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:01:55.029][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:55.030][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:01:55.031][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-06 16:01:55.031][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:01:55.032][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:55.033][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-09-06 16:01:55.034][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:01:55.035][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-09-06 16:01:55.035][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-09-06 16:01:55.036][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:01:55.036][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:01:55.037][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-09-06 16:01:55.038][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:55.039][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:55.040][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:01:55.040][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:01:55.041][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:01:55.042][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:01:55.043][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-09-06 16:01:55.043][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-09-06 16:01:55.043][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-09-06 16:01:55.043][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:01:55.044][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:01:55.045][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:01:55.046][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-09-06 16:01:55.047][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-09-06 16:01:55.048][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-06 16:01:55.049][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-06 16:01:55.051][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-09-06 16:01:55.052][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-06 16:01:55.053][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-09-06 16:01:55.058][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2025-09-06 16:01:55.066][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2025-09-06 16:01:55.070][biodb::testThat]
biodb.INFO [2025-09-06 16:01:55.070][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-09-06 16:01:55.071][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:55.072][biodb::testThat]
biodb.TRACE[2025-09-06 16:01:55.074][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2025-09-06 16:01:55.075][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-09-06 16:01:55.077][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-09-06 16:01:55.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-06 16:01:55.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:55.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:55.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:55.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:55.086][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:55.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-06 16:01:55.089][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.090][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.092][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.101][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.102][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.104][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.105][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.108][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.111][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.117][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:01:55.139][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2025-09-06 16:01:55.141][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:55.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:55.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.144][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:55.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:55.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.148][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:55.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:55.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.151][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:01:55.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:01:55.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.154][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:01:55.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:01:55.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.158][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-06 16:01:55.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-06 16:01:55.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.161][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-06 16:01:55.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-06 16:01:55.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.172][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.205][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.208][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.212][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.230][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.231][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.232][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.244][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.247][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.251][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.254][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.255][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.256][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.257][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.257][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.268][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.269][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.271][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.280][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.281][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.283][ef$get] fields variable is a list.
biodb.INFO [2025-09-06 16:01:55.290][biodb::testThat]
biodb.INFO [2025-09-06 16:01:55.291][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-09-06 16:01:55.292][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:55.293][biodb::testThat]
biodb.DEBUG[2025-09-06 16:01:55.295][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-09-06 16:01:55.300][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-09-06 16:01:55.302][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
fscache.DEBUG[2025-09-06 16:01:55.305][FUN] Found encoding ISO-8859-1 for file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75/3.xml.
biodb.DEBUG[2025-09-06 16:01:55.307][conn$getEntryContent] 1 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:01:55.308][self$createEntryFromContent] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-09-06 16:01:55.309][self$createEntryFromContent] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-09-06 16:01:55.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-06 16:01:55.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:55.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:55.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:55.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:55.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:55.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-06 16:01:55.320][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.321][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.322][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.322][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.341][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.342][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.343][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.344][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:01:55.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.348][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.351][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.357][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-09-06 16:01:55.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:01:55.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:01:55.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:01:55.385][self$createEntryFromContent] Accession numbers: 3.
biodb.TRACE[2025-09-06 16:01:55.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-09-06 16:01:55.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-09-06 16:01:55.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-09-06 16:01:55.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-09-06 16:01:55.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-09-06 16:01:55.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-09-06 16:01:55.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-09-06 16:01:55.403][biodb::testThat]
biodb.INFO [2025-09-06 16:01:55.404][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-09-06 16:01:55.405][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:55.405][biodb::testThat]
biodb.INFO [2025-09-06 16:01:55.411][biodb::testThat]
biodb.INFO [2025-09-06 16:01:55.412][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-09-06 16:01:55.413][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:55.414][biodb::testThat]
biodb.WARN [2025-09-06 16:01:55.417][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-09-06 16:01:55.420][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-09-06 16:01:55.428][biodb::testThat]
biodb.INFO [2025-09-06 16:01:55.429][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-09-06 16:01:55.430][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:55.430][biodb::testThat]
biodb.TRACE[2025-09-06 16:01:55.439][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:55.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:55.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.442][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:55.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:55.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.446][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:55.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:55.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.449][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:01:55.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:01:55.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.452][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:01:55.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:01:55.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.455][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-06 16:01:55.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-06 16:01:55.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.459][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-06 16:01:55.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-06 16:01:55.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.474][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:55.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:55.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.477][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-09-06 16:01:55.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-09-06 16:01:55.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.481][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:55.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-09-06 16:01:55.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.484][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:01:55.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:01:55.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.487][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:01:55.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:01:55.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.491][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-06 16:01:55.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-06 16:01:55.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:01:55.494][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-06 16:01:55.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-06 16:01:55.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:01:55.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-09-06 16:01:55.503][biodb::testThat]
biodb.INFO [2025-09-06 16:01:55.504][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-09-06 16:01:55.504][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:55.505][biodb::testThat]
biodb.INFO [2025-09-06 16:01:55.517][biodb::testThat]
biodb.INFO [2025-09-06 16:01:55.518][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-09-06 16:01:55.519][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:55.520][biodb::testThat]
biodb.INFO [2025-09-06 16:01:55.532][biodb::testThat]
biodb.INFO [2025-09-06 16:01:55.533][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-09-06 16:01:55.533][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:55.534][biodb::testThat]
biodb.INFO [2025-09-06 16:01:55.551][biodb::testThat]
biodb.INFO [2025-09-06 16:01:55.552][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-09-06 16:01:55.553][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:01:55.554][biodb::testThat]
biodb.INFO [2025-09-06 16:01:55.566][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-09-06 16:01:55.567][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2025-09-06 16:01:55.568][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-06 16:01:55.569][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:01:55.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:01:55.570][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:01:55.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:01:55.572][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:01:55.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 29 | WARN 1 | SKIP 0 | PASS 252 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_ccds.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$doGetEntryContentOneByOne(id)
  9.               └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 11.                   └─self$getEntryPageUrl(id)
 12.                     └─private$doGetEntryPageUrl(entry.id)
 13.                       └─base::vapply(id, fct, FUN.VALUE = "")
 14.                         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$doGetEntryContentOneByOne(id)
 11.                   └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 13.                       └─self$getEntryPageUrl(id)
 14.                         └─private$doGetEntryPageUrl(entry.id)
 15.                           └─base::vapply(id, fct, FUN.VALUE = "")
 16.                             └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): Entry fields have a correct value ──────
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─opt$refEntries$saveEntriesAsJson(id, list(e))
  4.     └─private$bdb$saveEntriesAsJson(entries, json.files)
  5.       └─entries[[i]]$getFieldsAsJson(compute = compute)
  6.         └─self$computeFields()
  7.           └─private$computeField(f)
  8.             └─self$getBiodb()$getFactory()$getEntry(db, id = db.id)
  9.               └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 10.                 └─conn$getEntryContent(ids)
 11.                   └─self$getEntryContentFromDb(ch.missing.ids)
 12.                     └─private$doGetEntryContentFromDb(entry.id)
 13.                       └─private$doGetEntryContentOneByOne(id)
 14.                         └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 15.                           └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 16.                             └─self$getEntryPageUrl(id)
 17.                               └─private$doGetEntryPageUrl(entry.id)
 18.                                 └─base::vapply(id, fct, FUN.VALUE = "")
 19.                                   └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 11.                   └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by searchable field ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 12.                     └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by name. ────
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 12.                     └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 13.                       └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by searchable field ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by name. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can get a URL pointing to the entry image. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry image URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for a compound ───
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(db = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─db$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() accepts a single vector. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): ppm tolerance works in annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): Input data frame is not modified by annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() works correctly with real values. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): Additional fields are accepted in annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry image. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry image URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)

[ FAIL 29 | WARN 1 | SKIP 0 | PASS 252 ]
Error: Test failures
In addition: Warning message:
In fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNcbi/DESCRIPTION’ ... OK
* this is package ‘biodbNcbi’ version ‘1.13.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNcbi’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    testref   7.6Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NcbiCcdsConn.Rd: BiodbFactory, BiodbConn
  NcbiCcdsEntry.Rd: BiodbHtmlEntry
  NcbiEntrezConn.Rd: BiodbConn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... WARNING
'library' or 'require' call not declared from: ‘biodbNci’
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
  
  [ FAIL 29 | WARN 1 | SKIP 0 | PASS 252 ]
  Error: Test failures
  In addition: Warning message:
  In fun(libname, pkgname) :
    Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
    version 3.23
  Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/00check.log’
for details.

Installation output

biodbNcbi.Rcheck/00install.out

* installing *source* package ‘biodbNcbi’ ...
** this is package ‘biodbNcbi’ version ‘1.13.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNcbi)