Back to Long Tests report for BioC 3.22

This page was generated on 2026-03-07 23:55 -0500 (Sat, 07 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4892
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4684
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 7/31HostnameOS / ArchCHECK
biodbNcbi 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-03-07 09:55 -0500 (Sat, 07 Mar 2026)
git_url: https://git.bioconductor.org/packages/biodbNcbi
git_branch: RELEASE_3_22
git_last_commit: dc1f90a
git_last_commit_date: 2025-10-29 11:15:40 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNcbi on merida1

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: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2026-03-07 16:01:50 -0500 (Sat, 07 Mar 2026)
EndedAt: 2026-03-07 16:03:02 -0500 (Sat, 07 Mar 2026)
EllapsedTime: 72.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNcbi.Rcheck
Warnings: NA

Tests output

biodbNcbi.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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 [2026-03-07 16:02:49.839][biodb::testContext]
biodb.INFO [2026-03-07 16:02:49.843][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-07 16:02:49.844][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2026-03-07 16:02:49.845][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-07 16:02:49.847][biodb::testContext]
biodb.INFO [2026-03-07 16:02:49.853][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-07 16:02:49.856][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-03-07 16:02:49.863][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:02:49.865][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-07 16:02:49.866][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-07 16:02:49.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:49.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:49.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:49.871][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-07 16:02:49.896][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-07 16:02:49.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:49.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:49.899][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[2026-03-07 16:02:49.900][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-07 16:02:49.902][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-07 16:02:49.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:49.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:49.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:49.906][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-07 16:02:49.908][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-07 16:02:49.909][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-07 16:02:49.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:49.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:49.912][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[2026-03-07 16:02:49.914][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-07 16:02:49.915][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-07 16:02:49.916][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-07 16:02:49.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:49.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:49.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:49.921][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-07 16:02:49.922][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-07 16:02:49.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:49.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:49.925][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[2026-03-07 16:02:49.927][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-07 16:02:49.928][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-07 16:02:49.929][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-07 16:02:49.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:49.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:49.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:49.934][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-07 16:02:49.935][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-07 16:02:49.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:49.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:49.938][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[2026-03-07 16:02:49.940][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-07 16:02:49.941][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-07 16:02:49.942][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-07 16:02:49.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:49.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:49.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:49.947][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-07 16:02:49.948][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-07 16:02:49.949][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-07 16:02:49.951][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-07 16:02:49.952][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-07 16:02:49.953][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-07 16:02:49.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:49.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:49.956][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[2026-03-07 16:02:49.958][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-07 16:02:49.959][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-07 16:02:49.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:49.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:49.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:49.964][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-07 16:02:49.965][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-07 16:02:49.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:49.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:49.968][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[2026-03-07 16:02:49.969][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-07 16:02:49.971][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-07 16:02:49.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:49.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:49.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:49.975][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-07 16:02:49.977][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-07 16:02:49.978][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-07 16:02:49.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:49.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:49.981][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[2026-03-07 16:02:49.983][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-07 16:02:49.984][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-07 16:02:49.994][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-07 16:02:49.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:49.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:49.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:49.999][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-07 16:02:50.001][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-07 16:02:50.002][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-07 16:02:50.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.005][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[2026-03-07 16:02:50.009][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-07 16:02:50.051][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:50.079][self$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[2026-03-07 16:02:50.081][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.082][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:50.083][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.085][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.086][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:50.087][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.088][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-07 16:02:50.090][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:50.091][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.092][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-07 16:02:50.094][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:50.095][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:50.096][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.098][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:50.098][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:02:50.098][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:02:50.098][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-07 16:02:50.098][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-07 16:02:50.099][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:50.100][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:50.101][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:50.103][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:50.104][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:50.105][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:50.106][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.108][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:50.109][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:50.110][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:50.111][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:50.112][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:50.114][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-07 16:02:50.116][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:50.117][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-07 16:02:50.119][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.120][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:50.121][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.123][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.124][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:50.125][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.126][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-07 16:02:50.128][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:50.129][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.130][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-07 16:02:50.131][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:50.133][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:50.134][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.135][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:50.135][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:02:50.135][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:02:50.135][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-07 16:02:50.135][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-07 16:02:50.137][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:50.138][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:50.139][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:50.140][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:50.141][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:50.142][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:50.144][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.145][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:50.146][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:50.147][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:50.148][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:50.150][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:50.151][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-07 16:02:50.153][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.155][self$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[2026-03-07 16:02:50.156][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.157][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:50.158][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.160][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.161][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:50.162][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.163][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-07 16:02:50.165][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:50.166][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:50.167][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-07 16:02:50.169][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:50.170][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:50.171][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.172][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:50.174][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:50.175][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:50.176][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:50.177][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:50.178][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:50.180][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:50.181][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.182][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:50.183][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:50.184][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:50.186][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:50.187][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:50.188][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-07 16:02:50.191][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.192][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-07 16:02:50.193][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.194][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:50.196][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.197][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.198][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:50.199][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.201][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-07 16:02:50.202][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:50.203][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:50.205][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-07 16:02:50.206][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:50.207][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:50.208][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.210][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:50.211][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:50.212][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:50.213][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:50.215][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:50.216][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:50.217][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:50.218][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.219][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:50.221][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:50.222][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:50.223][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:50.224][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:50.228][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:02:50.229][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.231][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[2026-03-07 16:02:50.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.236][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[2026-03-07 16:02:50.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.242][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[2026-03-07 16:02:50.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.248][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[2026-03-07 16:02:50.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.254][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[2026-03-07 16:02:50.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.259][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[2026-03-07 16:02:50.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.265][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[2026-03-07 16:02:50.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.271][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[2026-03-07 16:02:50.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.277][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[2026-03-07 16:02:50.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.282][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[2026-03-07 16:02:50.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.288][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[2026-03-07 16:02:50.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.294][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[2026-03-07 16:02:50.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.300][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[2026-03-07 16:02:50.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.305][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[2026-03-07 16:02:50.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.311][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[2026-03-07 16:02:50.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.317][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[2026-03-07 16:02:50.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.323][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[2026-03-07 16:02:50.324][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-07 16:02:50.333][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-07 16:02:50.335][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-07 16:02:50.337][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-07 16:02:50.339][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-07 16:02:50.340][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-07 16:02:50.342][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-07 16:02:50.344][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-07 16:02:50.345][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-07 16:02:50.347][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-07 16:02:50.349][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-07 16:02:50.351][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-07 16:02:50.352][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-07 16:02:50.354][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-07 16:02:50.356][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-07 16:02:50.358][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-07 16:02:50.359][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-07 16:02:50.361][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-07 16:02:50.363][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-07 16:02:50.364][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-07 16:02:50.366][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-07 16:02:50.368][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-07 16:02:50.370][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-07 16:02:50.371][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-07 16:02:50.373][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-07 16:02:50.375][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-07 16:02:50.376][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-07 16:02:50.378][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-07 16:02:50.380][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-07 16:02:50.382][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-07 16:02:50.383][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-07 16:02:50.385][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-07 16:02:50.387][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-07 16:02:50.389][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-07 16:02:50.390][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-07 16:02:50.392][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-07 16:02:50.394][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-07 16:02:50.395][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-07 16:02:50.397][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-07 16:02:50.399][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-07 16:02:50.401][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-07 16:02:50.402][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-07 16:02:50.404][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-07 16:02:50.406][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-07 16:02:50.408][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-07 16:02:50.409][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-07 16:02:50.411][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-07 16:02:50.413][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-07 16:02:50.415][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-07 16:02:50.416][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-07 16:02:50.418][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-07 16:02:50.420][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-07 16:02:50.421][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-07 16:02:50.423][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-07 16:02:50.425][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-07 16:02:50.427][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-07 16:02:50.428][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-07 16:02:50.430][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-07 16:02:50.432][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-07 16:02:50.434][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-07 16:02:50.435][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-07 16:02:50.437][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-07 16:02:50.439][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-07 16:02:50.440][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-07 16:02:50.442][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-07 16:02:50.444][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-07 16:02:50.446][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-07 16:02:50.447][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-07 16:02:50.449][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-07 16:02:50.451][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-07 16:02:50.453][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-07 16:02:50.454][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-07 16:02:50.456][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-07 16:02:50.458][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-07 16:02:50.460][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-07 16:02:50.461][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-07 16:02:50.463][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-07 16:02:50.465][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-07 16:02:50.467][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-07 16:02:50.469][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-07 16:02:50.470][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-07 16:02:50.472][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-07 16:02:50.474][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-07 16:02:50.481][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-07 16:02:50.483][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-07 16:02:50.487][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:02:50.488][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.490][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.491][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[2026-03-07 16:02:50.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:50.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:50.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.504][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[2026-03-07 16:02:50.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:50.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:50.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.512][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[2026-03-07 16:02:50.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:50.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:50.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.520][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[2026-03-07 16:02:50.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:50.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:50.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.528][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[2026-03-07 16:02:50.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:50.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:50.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.536][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[2026-03-07 16:02:50.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:50.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:50.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.544][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[2026-03-07 16:02:50.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:50.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:50.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.552][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[2026-03-07 16:02:50.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:50.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:50.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.559][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[2026-03-07 16:02:50.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:50.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:50.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.567][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[2026-03-07 16:02:50.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:50.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:50.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.575][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[2026-03-07 16:02:50.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:50.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:50.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.589][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[2026-03-07 16:02:50.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:50.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:50.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.597][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[2026-03-07 16:02:50.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:50.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:50.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.605][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[2026-03-07 16:02:50.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:50.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:50.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.613][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[2026-03-07 16:02:50.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:50.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:50.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.621][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[2026-03-07 16:02:50.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:50.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:50.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:50.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.629][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[2026-03-07 16:02:50.631][bdb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-03-07 16:02:50.645][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-03-07 16:02:50.647][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.649][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-03-07 16:02:50.650][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.651][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:50.653][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.654][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.655][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.656][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.658][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-03-07 16:02:50.659][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:50.660][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.662][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-03-07 16:02:50.663][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:50.664][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-03-07 16:02:50.664][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-03-07 16:02:50.666][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:50.667][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:50.668][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-07 16:02:50.670][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:50.671][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:50.672][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:50.673][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:50.674][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:50.676][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.677][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-03-07 16:02:50.677][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-03-07 16:02:50.678][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:50.679][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:50.681][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.682][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:50.684][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-03-07 16:02:50.686][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.687][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-03-07 16:02:50.688][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.690][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:50.691][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.692][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.693][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.695][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.696][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-07 16:02:50.697][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:50.699][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.700][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-03-07 16:02:50.701][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:50.702][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-03-07 16:02:50.702][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-03-07 16:02:50.702][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-03-07 16:02:50.702][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-03-07 16:02:50.702][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-03-07 16:02:50.702][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-03-07 16:02:50.704][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:50.705][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:50.706][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-07 16:02:50.707][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:50.709][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:50.710][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:50.711][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:50.712][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:50.713][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.715][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:50.715][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-07 16:02:50.716][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:50.717][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:50.718][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.720][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:50.721][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-03-07 16:02:50.724][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:50.725][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-03-07 16:02:50.726][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.727][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:50.729][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.730][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.731][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.733][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.734][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-07 16:02:50.735][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:50.737][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.738][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-03-07 16:02:50.739][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:50.740][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-03-07 16:02:50.740][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:50.740][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:50.740][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:50.740][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:50.740][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:50.740][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:50.740][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:50.740][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:50.740][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:50.740][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-03-07 16:02:50.740][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:50.740][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:50.740][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:50.742][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:50.744][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:50.744][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:02:50.744][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:02:50.745][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-03-07 16:02:50.746][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:50.747][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:50.749][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:50.750][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:50.751][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:50.752][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.754][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:50.754][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-07 16:02:50.754][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-03-07 16:02:50.755][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:50.756][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:50.758][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.759][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-03-07 16:02:50.760][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-03-07 16:02:50.763][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.764][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-03-07 16:02:50.765][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.767][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:50.768][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.769][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.770][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.772][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.773][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-07 16:02:50.774][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:50.775][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.777][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-03-07 16:02:50.778][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:50.779][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-03-07 16:02:50.779][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-03-07 16:02:50.781][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:50.782][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:50.783][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-03-07 16:02:50.785][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:50.786][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:50.787][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:50.788][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:50.789][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:50.790][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:50.792][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:50.792][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-07 16:02:50.792][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-03-07 16:02:50.793][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:50.794][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:50.795][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:50.797][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-03-07 16:02:50.804][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-03-07 16:02:50.806][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-07 16:02:50.808][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-07 16:02:50.810][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-03-07 16:02:50.812][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-07 16:02:50.814][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-03-07 16:02:50.834][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2026-03-07 16:02:50.849][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2026-03-07 16:02:50.864][biodb::testThat]
biodb.INFO [2026-03-07 16:02:50.865][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-03-07 16:02:50.867][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:50.868][biodb::testThat]
biodb.TRACE[2026-03-07 16:02:50.872][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2026-03-07 16:02:50.874][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2026-03-07 16:02:50.877][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2026-03-07 16:02:50.885][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-07 16:02:50.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:50.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:50.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:50.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:50.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:50.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-07 16:02:50.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:50.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:50.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:50.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:50.948][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-03-07 16:02:50.965][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:50.967][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:50.968][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.005][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-03-07 16:02:51.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.010][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.016][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.026][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-07 16:02:51.118][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2026-03-07 16:02:51.121][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.126][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.163][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-07 16:02:51.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-07 16:02:51.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.169][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-07 16:02:51.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-07 16:02:51.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.174][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-07 16:02:51.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-07 16:02:51.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.179][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-07 16:02:51.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-07 16:02:51.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.208][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.253][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.258][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.264][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.293][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.295][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.296][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.297][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.314][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-03-07 16:02:51.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.320][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.329][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.334][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-03-07 16:02:51.335][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.336][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.338][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.339][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-03-07 16:02:51.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.355][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.356][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.358][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.359][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.365][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.367][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.368][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.369][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.393][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2026-03-07 16:02:51.440][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2026-03-07 16:02:51.442][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2026-03-07 16:02:51.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-07 16:02:51.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:51.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:51.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:51.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:51.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:51.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-07 16:02:51.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.500][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-03-07 16:02:51.502][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.503][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.504][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.506][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-03-07 16:02:51.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.511][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.516][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.527][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-07 16:02:51.598][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2026-03-07 16:02:51.625][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.630][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.635][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-07 16:02:51.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-07 16:02:51.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.640][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-07 16:02:51.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-07 16:02:51.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.645][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-07 16:02:51.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-07 16:02:51.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.650][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-07 16:02:51.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-07 16:02:51.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.666][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.710][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.715][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.720][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:51.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.762][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.764][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.765][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.766][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.783][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-03-07 16:02:51.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.792][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.797][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.802][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-03-07 16:02:51.803][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.805][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.806][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.807][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-03-07 16:02:51.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.823][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.824][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:51.826][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.827][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:51.834][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:51.835][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:51.836][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:51.837][ef$get] fields variable is a list.
biodb.INFO [2026-03-07 16:02:51.848][biodb::testThat]
biodb.INFO [2026-03-07 16:02:51.849][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-03-07 16:02:51.851][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:51.852][biodb::testThat]
biodb.DEBUG[2026-03-07 16:02:51.855][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2026-03-07 16:02:51.860][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2026-03-07 16:02:51.864][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-03-07 16:02:51.865][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:02:51.867][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-03-07 16:02:51.868][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:02:51.869][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-03-07 16:02:52.054][biodb::testThat]
biodb.INFO [2026-03-07 16:02:52.056][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-03-07 16:02:52.057][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:52.058][biodb::testThat]
biodb.INFO [2026-03-07 16:02:52.067][biodb::testThat]
biodb.INFO [2026-03-07 16:02:52.068][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-03-07 16:02:52.069][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:52.070][biodb::testThat]
biodb.WARN [2026-03-07 16:02:52.092][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-03-07 16:02:52.118][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-03-07 16:02:52.129][biodb::testThat]
biodb.INFO [2026-03-07 16:02:52.130][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-03-07 16:02:52.131][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:52.132][biodb::testThat]
biodb.DEBUG[2026-03-07 16:02:52.156][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2026-03-07 16:02:52.227][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2026-03-07 16:02:52.269][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-03-07 16:02:52.270][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:02:52.272][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-03-07 16:02:52.273][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:02:52.274][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-03-07 16:02:52.369][biodb::testThat]
biodb.INFO [2026-03-07 16:02:52.371][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-03-07 16:02:52.372][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:52.373][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-03-07 16:02:52.462][biodb::testThat]
biodb.INFO [2026-03-07 16:02:52.463][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-03-07 16:02:52.464][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:52.465][biodb::testThat]
biodb.INFO [2026-03-07 16:02:52.476][biodb::testThat]
biodb.INFO [2026-03-07 16:02:52.478][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-03-07 16:02:52.479][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:52.480][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-03-07 16:02:52.540][biodb::testThat]
biodb.INFO [2026-03-07 16:02:52.541][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-03-07 16:02:52.542][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:52.543][biodb::testThat]
biodb.INFO [2026-03-07 16:02:52.552][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-07 16:02:52.553][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2026-03-07 16:02:52.554][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-07 16:02:52.555][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:52.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:52.558][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:52.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:52.560][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-03-07 16:02:52.574][biodb::testContext]
biodb.INFO [2026-03-07 16:02:52.576][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-07 16:02:52.577][biodb::testContext] Test context - Gene long tests
biodb.INFO [2026-03-07 16:02:52.578][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-07 16:02:52.579][biodb::testContext]
biodb.INFO [2026-03-07 16:02:52.582][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-07 16:02:52.584][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-03-07 16:02:52.589][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:02:52.590][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-07 16:02:52.592][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-07 16:02:52.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.595][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[2026-03-07 16:02:52.596][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-07 16:02:52.603][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-07 16:02:52.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:52.607][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-07 16:02:52.609][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-07 16:02:52.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.612][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[2026-03-07 16:02:52.613][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-07 16:02:52.615][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-07 16:02:52.616][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-07 16:02:52.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:52.620][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-07 16:02:52.622][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-07 16:02:52.623][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-07 16:02:52.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.626][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[2026-03-07 16:02:52.628][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-07 16:02:52.629][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-07 16:02:52.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:52.634][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-07 16:02:52.635][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-07 16:02:52.636][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-07 16:02:52.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.639][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[2026-03-07 16:02:52.641][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-07 16:02:52.642][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-07 16:02:52.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:52.647][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-07 16:02:52.648][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-07 16:02:52.649][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-07 16:02:52.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.652][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[2026-03-07 16:02:52.654][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-07 16:02:52.655][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-07 16:02:52.656][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-07 16:02:52.658][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-07 16:02:52.659][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-07 16:02:52.660][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-07 16:02:52.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:52.665][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-07 16:02:52.666][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-07 16:02:52.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.670][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[2026-03-07 16:02:52.671][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-07 16:02:52.672][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-07 16:02:52.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:52.677][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-07 16:02:52.678][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-07 16:02:52.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.682][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[2026-03-07 16:02:52.683][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-07 16:02:52.684][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-07 16:02:52.686][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-07 16:02:52.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:52.690][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-07 16:02:52.691][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-07 16:02:52.702][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-07 16:02:52.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.705][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[2026-03-07 16:02:52.706][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-07 16:02:52.708][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-07 16:02:52.709][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-07 16:02:52.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:52.714][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-07 16:02:52.716][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:52.717][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-03-07 16:02:52.719][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:52.720][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:52.721][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:52.722][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:52.724][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:52.725][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:52.726][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-07 16:02:52.727][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:52.729][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:52.730][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-07 16:02:52.731][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:52.732][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:52.734][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:52.735][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:52.735][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:02:52.735][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:02:52.735][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-07 16:02:52.735][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-07 16:02:52.736][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:52.737][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:52.739][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:52.740][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:52.741][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:52.742][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:52.743][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:52.745][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:52.746][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:52.747][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:52.748][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:52.749][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:52.751][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-07 16:02:52.753][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:52.754][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-07 16:02:52.756][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:52.757][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:52.758][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:52.759][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:52.761][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:52.762][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:52.763][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-07 16:02:52.764][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:52.766][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:52.767][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-07 16:02:52.768][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:52.769][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:52.771][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:52.772][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:52.772][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:02:52.772][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:02:52.772][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-07 16:02:52.772][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-07 16:02:52.773][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:52.775][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:52.776][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:52.777][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:52.778][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:52.779][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:52.780][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:52.782][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:52.783][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:52.784][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:52.785][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:52.787][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:52.788][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-07 16:02:52.790][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:52.792][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-03-07 16:02:52.793][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:52.795][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:52.796][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:52.797][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:52.799][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:52.800][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:52.801][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-07 16:02:52.803][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:52.804][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:52.805][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-07 16:02:52.810][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:52.812][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:52.813][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:52.814][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:52.816][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:52.817][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:52.818][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:52.820][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:52.821][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:52.822][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:52.823][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:52.824][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:52.826][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:52.827][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:52.828][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:52.830][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:52.831][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-07 16:02:52.833][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:52.834][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-07 16:02:52.836][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:52.837][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:52.838][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:52.840][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:52.841][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:52.842][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:52.843][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-07 16:02:52.845][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:52.846][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:52.847][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-07 16:02:52.848][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:52.850][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:52.851][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:52.852][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:52.853][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:52.855][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:52.856][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:52.857][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:52.858][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:52.859][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:52.860][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:52.862][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:52.863][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:52.864][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:52.865][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:52.867][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:52.868][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:02:52.869][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.870][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[2026-03-07 16:02:52.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:52.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:52.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.876][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[2026-03-07 16:02:52.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:52.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:52.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.882][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[2026-03-07 16:02:52.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:52.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:52.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.887][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[2026-03-07 16:02:52.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:52.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:52.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.893][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[2026-03-07 16:02:52.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:52.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:52.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.898][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[2026-03-07 16:02:52.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:52.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:52.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.904][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[2026-03-07 16:02:52.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:52.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:52.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.910][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[2026-03-07 16:02:52.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:52.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:52.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.915][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[2026-03-07 16:02:52.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:52.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:52.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.921][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[2026-03-07 16:02:52.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:52.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:52.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.926][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[2026-03-07 16:02:52.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:52.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:52.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.932][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[2026-03-07 16:02:52.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:52.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:52.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.938][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[2026-03-07 16:02:52.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:52.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:52.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.943][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[2026-03-07 16:02:52.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:52.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:52.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.949][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[2026-03-07 16:02:52.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:52.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:52.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.955][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[2026-03-07 16:02:52.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:52.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:52.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:52.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:52.960][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[2026-03-07 16:02:52.961][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-07 16:02:52.963][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-07 16:02:52.965][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-07 16:02:52.967][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-07 16:02:52.968][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-07 16:02:52.970][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-07 16:02:52.972][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-07 16:02:52.973][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-07 16:02:52.975][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-07 16:02:52.977][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-07 16:02:52.979][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-07 16:02:52.981][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-07 16:02:52.982][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-07 16:02:52.984][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-07 16:02:52.986][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-07 16:02:52.987][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-07 16:02:52.989][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-07 16:02:52.991][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-07 16:02:52.993][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-07 16:02:52.994][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-07 16:02:52.996][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-07 16:02:52.998][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-07 16:02:53.000][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-07 16:02:53.006][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-07 16:02:53.008][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-07 16:02:53.010][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-07 16:02:53.012][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-07 16:02:53.013][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-07 16:02:53.015][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-07 16:02:53.017][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-07 16:02:53.019][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-07 16:02:53.021][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-07 16:02:53.024][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-07 16:02:53.026][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-07 16:02:53.028][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-07 16:02:53.030][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-07 16:02:53.031][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-07 16:02:53.033][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-07 16:02:53.035][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-07 16:02:53.037][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-07 16:02:53.038][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-07 16:02:53.040][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-07 16:02:53.042][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-07 16:02:53.043][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-07 16:02:53.045][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-07 16:02:53.047][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-07 16:02:53.048][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-07 16:02:53.050][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-07 16:02:53.052][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-07 16:02:53.054][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-07 16:02:53.055][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-07 16:02:53.057][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-07 16:02:53.059][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-07 16:02:53.060][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-07 16:02:53.062][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-07 16:02:53.064][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-07 16:02:53.065][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-07 16:02:53.067][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-07 16:02:53.069][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-07 16:02:53.070][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-07 16:02:53.072][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-07 16:02:53.074][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-07 16:02:53.076][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-07 16:02:53.077][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-07 16:02:53.079][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-07 16:02:53.081][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-07 16:02:53.082][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-07 16:02:53.084][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-07 16:02:53.086][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-07 16:02:53.087][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-07 16:02:53.089][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-07 16:02:53.091][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-07 16:02:53.092][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-07 16:02:53.094][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-07 16:02:53.096][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-07 16:02:53.098][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-07 16:02:53.099][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-07 16:02:53.101][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-07 16:02:53.103][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-07 16:02:53.104][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-07 16:02:53.106][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-07 16:02:53.108][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-07 16:02:53.109][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-07 16:02:53.111][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-07 16:02:53.113][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-07 16:02:53.114][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:02:53.115][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:53.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:53.118][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:53.119][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[2026-03-07 16:02:53.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:53.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:53.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:53.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:53.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:53.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:53.127][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[2026-03-07 16:02:53.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:53.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:53.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:53.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:53.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:53.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:53.134][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[2026-03-07 16:02:53.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:53.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:53.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:53.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:53.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:53.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:53.142][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[2026-03-07 16:02:53.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:53.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:53.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:53.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:53.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:53.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:53.150][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[2026-03-07 16:02:53.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:53.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:53.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:53.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:53.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:53.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:53.158][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[2026-03-07 16:02:53.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:53.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:53.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:53.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:53.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:53.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:53.166][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[2026-03-07 16:02:53.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:53.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:53.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:53.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:53.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:53.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:53.174][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[2026-03-07 16:02:53.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:53.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:53.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:53.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:53.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:53.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:53.181][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[2026-03-07 16:02:53.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:53.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:53.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:53.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:53.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:53.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:53.189][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[2026-03-07 16:02:53.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:53.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:53.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:53.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:53.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:53.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:53.201][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[2026-03-07 16:02:53.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:53.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:53.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:53.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:53.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:53.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:53.209][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[2026-03-07 16:02:53.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:53.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:53.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:53.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:53.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:53.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:53.216][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[2026-03-07 16:02:53.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:53.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:53.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:53.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:53.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:53.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:53.224][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[2026-03-07 16:02:53.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:53.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:53.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:53.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:53.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:53.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:53.232][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[2026-03-07 16:02:53.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:53.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:53.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:53.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:53.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:53.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:53.239][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[2026-03-07 16:02:53.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:53.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:53.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:53.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:53.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:53.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:53.247][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[2026-03-07 16:02:53.250][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-03-07 16:02:53.252][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-03-07 16:02:53.254][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.255][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-03-07 16:02:53.256][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.258][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:53.259][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.260][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:53.261][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.262][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:53.264][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-03-07 16:02:53.265][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:53.266][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.267][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-03-07 16:02:53.269][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:53.270][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-03-07 16:02:53.270][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-03-07 16:02:53.271][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:53.272][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:53.274][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-07 16:02:53.275][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:53.276][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:53.277][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:53.278][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:53.279][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:53.281][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:53.282][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-03-07 16:02:53.282][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-03-07 16:02:53.283][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:53.284][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:53.285][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.287][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:53.288][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-03-07 16:02:53.290][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.292][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-03-07 16:02:53.293][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.294][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:53.295][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.296][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:53.298][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.299][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:53.300][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-07 16:02:53.301][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:53.303][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.304][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-03-07 16:02:53.305][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:53.306][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-03-07 16:02:53.306][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-03-07 16:02:53.306][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-03-07 16:02:53.306][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-03-07 16:02:53.306][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-03-07 16:02:53.306][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-03-07 16:02:53.308][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:53.309][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:53.310][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-07 16:02:53.311][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:53.312][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:53.314][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:53.315][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:53.316][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:53.317][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:53.318][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:53.318][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-07 16:02:53.319][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:53.321][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:53.322][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.323][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:53.325][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-03-07 16:02:53.327][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:53.328][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-03-07 16:02:53.329][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.330][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:53.332][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.333][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:53.334][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.335][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:53.337][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-07 16:02:53.338][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:53.339][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.340][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-03-07 16:02:53.342][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:53.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-03-07 16:02:53.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:53.343][self$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[2026-03-07 16:02:53.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:53.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:53.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:53.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:53.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:53.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:53.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:53.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-03-07 16:02:53.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:53.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:53.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:53.344][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:53.346][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:53.346][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:02:53.346][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:02:53.347][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-03-07 16:02:53.348][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:53.349][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:53.351][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:53.352][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:53.353][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:53.354][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:53.355][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:53.355][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-07 16:02:53.355][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-03-07 16:02:53.357][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:53.358][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:53.359][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.360][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-03-07 16:02:53.362][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-03-07 16:02:53.364][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.366][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-03-07 16:02:53.367][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.368][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:53.369][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.371][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:53.372][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.373][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:53.374][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-07 16:02:53.376][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:53.377][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.378][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-03-07 16:02:53.379][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:53.381][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-03-07 16:02:53.381][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-03-07 16:02:53.382][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:53.383][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:53.384][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-03-07 16:02:53.386][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:53.391][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:53.392][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:53.393][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:53.394][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:53.395][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:53.397][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:53.397][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-07 16:02:53.397][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-03-07 16:02:53.398][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:53.399][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:53.400][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:53.401][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-03-07 16:02:53.403][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-03-07 16:02:53.405][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-07 16:02:53.407][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-07 16:02:53.408][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-03-07 16:02:53.410][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-07 16:02:53.412][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-03-07 16:02:53.421][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2026-03-07 16:02:53.460][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2026-03-07 16:02:53.465][biodb::testThat]
biodb.INFO [2026-03-07 16:02:53.466][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-03-07 16:02:53.467][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:53.468][biodb::testThat]
biodb.TRACE[2026-03-07 16:02:53.474][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2026-03-07 16:02:53.476][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2026-03-07 16:02:53.479][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2026-03-07 16:02:53.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-07 16:02:53.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:53.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:53.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:53.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:53.492][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:53.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-07 16:02:53.507][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:53.509][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:53.510][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.511][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:53.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:53.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.518][ef$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:02:53.520][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:02:53.521][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.522][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.524][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:02:53.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:02:53.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.529][ef$get] Asked field names are: location.
biodb.TRACE[2026-03-07 16:02:53.530][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2026-03-07 16:02:53.532][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.533][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.535][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2026-03-07 16:02:53.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2026-03-07 16:02:53.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.540][ef$get] Asked field names are: symbol.
biodb.TRACE[2026-03-07 16:02:53.541][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2026-03-07 16:02:53.542][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.543][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.545][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2026-03-07 16:02:53.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2026-03-07 16:02:53.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.551][ef$get] Asked field names are: synonyms.
biodb.TRACE[2026-03-07 16:02:53.552][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:53.553][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.554][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.556][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2026-03-07 16:02:53.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:53.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.562][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2026-03-07 16:02:53.563][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2026-03-07 16:02:53.564][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.565][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.568][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2026-03-07 16:02:53.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2026-03-07 16:02:53.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.579][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:53.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:53.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.584][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-03-07 16:02:53.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-03-07 16:02:53.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.589][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-03-07 16:02:53.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-03-07 16:02:53.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:53.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:53.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.599][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-03-07 16:02:53.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-03-07 16:02:53.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:53.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:53.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:53.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:53.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:53.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:53.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:53.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:53.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:53.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:53.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:53.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:53.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-07 16:02:53.641][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2026-03-07 16:02:53.644][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-07 16:02:53.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:53.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.649][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-07 16:02:53.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:53.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.654][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:53.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:53.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.659][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:53.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:53.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:53.664][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:53.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:53.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-07 16:02:53.669][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2026-03-07 16:02:53.709][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2026-03-07 16:02:53.729][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2026-03-07 16:02:53.730][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2026-03-07 16:02:53.735][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2026-03-07 16:02:53.737][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-03-07 16:02:53.738][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:02:53.740][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-03-07 16:02:53.741][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:02:53.742][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-03-07 16:02:53.807][biodb::testThat]
biodb.INFO [2026-03-07 16:02:53.808][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-03-07 16:02:53.809][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:53.810][biodb::testThat]
biodb.DEBUG[2026-03-07 16:02:53.813][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2026-03-07 16:02:53.815][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2026-03-07 16:02:53.817][cch$loadContents] Load 8 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-03-07 16:02:53.818][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:02:53.820][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:53.821][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:02:53.822][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-07 16:02:53.823][private$retrieveContents] Get entry content(s) for 8 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-03-07 16:02:53.884][biodb::testThat]
biodb.INFO [2026-03-07 16:02:53.885][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-03-07 16:02:53.886][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:53.887][biodb::testThat]
biodb.TRACE[2026-03-07 16:02:53.891][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:53.893][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:53.894][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:53.895][ef$get] fields variable is a list.
biodb.DEBUG[2026-03-07 16:02:53.897][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2026-03-07 16:02:53.908][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-03-07 16:02:53.909][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-03-07 16:02:53.911][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-03-07 16:02:53.912][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:02:53.914][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:53.915][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:02:53.916][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-07 16:02:53.939][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-03-07 16:02:54.022][biodb::testThat]
biodb.INFO [2026-03-07 16:02:54.023][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-03-07 16:02:54.024][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:54.026][biodb::testThat]
biodb.DEBUG[2026-03-07 16:02:54.036][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-03-07 16:02:54.037][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-03-07 16:02:54.039][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-03-07 16:02:54.041][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:02:54.042][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:54.043][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:02:54.044][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-07 16:02:54.046][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-03-07 16:02:54.105][biodb::testThat]
biodb.INFO [2026-03-07 16:02:54.107][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-03-07 16:02:54.108][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:54.109][biodb::testThat]
biodb.DEBUG[2026-03-07 16:02:54.115][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-03-07 16:02:54.116][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-03-07 16:02:54.118][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-03-07 16:02:54.120][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:02:54.121][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:54.122][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:02:54.124][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-07 16:02:54.125][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-03-07 16:02:54.191][biodb::testThat]
biodb.INFO [2026-03-07 16:02:54.192][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-03-07 16:02:54.193][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:54.195][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-03-07 16:02:54.255][biodb::testThat]
biodb.INFO [2026-03-07 16:02:54.257][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-03-07 16:02:54.258][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:54.259][biodb::testThat]
biodb.INFO [2026-03-07 16:02:54.272][biodb::testThat]
biodb.INFO [2026-03-07 16:02:54.273][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-03-07 16:02:54.274][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:54.275][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-03-07 16:02:54.346][biodb::testThat]
biodb.INFO [2026-03-07 16:02:54.347][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-03-07 16:02:54.348][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:54.350][biodb::testThat]
biodb.INFO [2026-03-07 16:02:54.358][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-07 16:02:54.360][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2026-03-07 16:02:54.361][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2026-03-07 16:02:54.362][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-07 16:02:54.364][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:54.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:54.366][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.368][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-03-07 16:02:54.375][biodb::testContext]
biodb.INFO [2026-03-07 16:02:54.376][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-07 16:02:54.378][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2026-03-07 16:02:54.379][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-07 16:02:54.380][biodb::testContext]
biodb.INFO [2026-03-07 16:02:54.383][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-07 16:02:54.384][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-03-07 16:02:54.389][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:02:54.390][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-07 16:02:54.392][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-07 16:02:54.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.396][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[2026-03-07 16:02:54.397][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-07 16:02:54.398][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-07 16:02:54.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:54.403][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-07 16:02:54.404][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-07 16:02:54.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.408][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[2026-03-07 16:02:54.409][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-07 16:02:54.410][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-07 16:02:54.412][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-07 16:02:54.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:54.416][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-07 16:02:54.418][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-07 16:02:54.419][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-07 16:02:54.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.423][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[2026-03-07 16:02:54.424][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-07 16:02:54.425][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-07 16:02:54.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:54.430][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-07 16:02:54.431][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-07 16:02:54.432][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-07 16:02:54.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.436][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[2026-03-07 16:02:54.437][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-07 16:02:54.438][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-07 16:02:54.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:54.443][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-07 16:02:54.446][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-07 16:02:54.447][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-07 16:02:54.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.452][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[2026-03-07 16:02:54.453][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-07 16:02:54.455][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-07 16:02:54.457][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-07 16:02:54.459][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-07 16:02:54.460][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-07 16:02:54.463][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-07 16:02:54.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:54.469][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-07 16:02:54.470][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-07 16:02:54.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.474][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[2026-03-07 16:02:54.475][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-07 16:02:54.477][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-07 16:02:54.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:54.481][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-07 16:02:54.483][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-07 16:02:54.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.486][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[2026-03-07 16:02:54.487][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-07 16:02:54.488][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-07 16:02:54.490][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-07 16:02:54.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:54.494][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-07 16:02:54.495][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-07 16:02:54.506][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-07 16:02:54.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.510][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[2026-03-07 16:02:54.511][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-07 16:02:54.512][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-07 16:02:54.513][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-07 16:02:54.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:54.523][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-07 16:02:54.525][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:54.526][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-03-07 16:02:54.527][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:54.529][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:54.530][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:54.531][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:54.532][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:54.534][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:54.535][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-07 16:02:54.536][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:54.537][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:54.539][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-07 16:02:54.540][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:54.541][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:54.542][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:54.544][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:54.544][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:02:54.544][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:02:54.544][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-07 16:02:54.544][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-07 16:02:54.545][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:54.546][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:54.547][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:54.548][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:54.550][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:54.551][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:54.552][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:54.553][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:54.554][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:54.556][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:54.557][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:54.558][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:54.560][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-07 16:02:54.562][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:54.564][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-07 16:02:54.565][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:54.566][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:54.567][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:54.569][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:54.570][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:54.571][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:54.572][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-07 16:02:54.574][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:54.575][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:54.576][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-07 16:02:54.578][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:54.579][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:54.580][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:54.581][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:54.581][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:02:54.581][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:02:54.581][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-07 16:02:54.581][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-07 16:02:54.583][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:54.584][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:54.585][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:54.586][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:54.588][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:54.589][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:54.590][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:54.591][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:54.592][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:54.594][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:54.595][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:54.597][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:54.598][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-07 16:02:54.607][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:54.608][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-03-07 16:02:54.609][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:54.610][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:54.612][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:54.613][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:54.614][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:54.615][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:54.617][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-07 16:02:54.618][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:54.619][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:54.621][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-07 16:02:54.622][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:54.623][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:54.624][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:54.626][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:54.627][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:54.628][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:54.629][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:54.631][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:54.632][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:54.633][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:54.634][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:54.635][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:54.637][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:54.638][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:54.639][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:54.640][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:54.642][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-07 16:02:54.644][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:54.645][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-07 16:02:54.646][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:54.648][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:54.649][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:54.650][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:54.651][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:54.653][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:54.654][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-07 16:02:54.655][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:54.657][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:54.658][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-07 16:02:54.659][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:54.660][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:54.662][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:54.663][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:54.664][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:54.665][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:54.667][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:54.668][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:54.669][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:54.671][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:54.672][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:54.673][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:54.674][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:54.676][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:54.677][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:54.680][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:54.681][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:02:54.683][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.684][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[2026-03-07 16:02:54.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.696][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[2026-03-07 16:02:54.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.702][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[2026-03-07 16:02:54.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.717][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[2026-03-07 16:02:54.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.726][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[2026-03-07 16:02:54.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.736][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[2026-03-07 16:02:54.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.742][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[2026-03-07 16:02:54.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.747][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[2026-03-07 16:02:54.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.753][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[2026-03-07 16:02:54.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.759][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[2026-03-07 16:02:54.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.765][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[2026-03-07 16:02:54.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.770][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[2026-03-07 16:02:54.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.776][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[2026-03-07 16:02:54.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.782][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[2026-03-07 16:02:54.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.788][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[2026-03-07 16:02:54.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.793][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[2026-03-07 16:02:54.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.799][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[2026-03-07 16:02:54.800][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-07 16:02:54.802][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-07 16:02:54.803][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-07 16:02:54.805][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-07 16:02:54.807][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-07 16:02:54.808][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-07 16:02:54.810][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-07 16:02:54.812][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-07 16:02:54.813][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-07 16:02:54.815][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-07 16:02:54.817][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-07 16:02:54.818][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-07 16:02:54.820][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-07 16:02:54.822][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-07 16:02:54.824][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-07 16:02:54.825][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-07 16:02:54.827][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-07 16:02:54.829][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-07 16:02:54.830][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-07 16:02:54.832][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-07 16:02:54.834][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-07 16:02:54.835][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-07 16:02:54.837][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-07 16:02:54.839][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-07 16:02:54.841][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-07 16:02:54.842][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-07 16:02:54.844][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-07 16:02:54.846][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-07 16:02:54.847][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-07 16:02:54.849][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-07 16:02:54.851][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-07 16:02:54.852][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-07 16:02:54.854][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-07 16:02:54.856][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-07 16:02:54.857][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-07 16:02:54.859][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-07 16:02:54.861][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-07 16:02:54.862][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-07 16:02:54.864][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-07 16:02:54.866][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-07 16:02:54.868][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-07 16:02:54.869][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-07 16:02:54.871][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-07 16:02:54.873][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-07 16:02:54.874][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-07 16:02:54.876][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-07 16:02:54.878][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-07 16:02:54.879][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-07 16:02:54.881][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-07 16:02:54.883][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-07 16:02:54.885][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-07 16:02:54.886][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-07 16:02:54.888][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-07 16:02:54.890][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-07 16:02:54.891][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-07 16:02:54.893][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-07 16:02:54.895][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-07 16:02:54.897][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-07 16:02:54.898][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-07 16:02:54.900][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-07 16:02:54.902][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-07 16:02:54.903][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-07 16:02:54.910][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-07 16:02:54.911][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-07 16:02:54.913][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-07 16:02:54.915][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-07 16:02:54.917][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-07 16:02:54.918][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-07 16:02:54.920][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-07 16:02:54.922][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-07 16:02:54.923][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-07 16:02:54.925][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-07 16:02:54.927][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-07 16:02:54.928][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-07 16:02:54.930][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-07 16:02:54.932][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-07 16:02:54.933][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-07 16:02:54.935][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-07 16:02:54.937][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-07 16:02:54.939][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-07 16:02:54.940][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-07 16:02:54.942][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-07 16:02:54.944][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-07 16:02:54.945][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-07 16:02:54.947][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-07 16:02:54.949][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:02:54.950][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.952][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.953][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[2026-03-07 16:02:54.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:54.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:54.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.961][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[2026-03-07 16:02:54.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:54.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:54.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.969][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[2026-03-07 16:02:54.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:54.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:54.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.976][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[2026-03-07 16:02:54.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:54.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:54.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.984][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[2026-03-07 16:02:54.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:54.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:54.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:54.992][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[2026-03-07 16:02:54.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:54.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:54.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:54.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:54.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:54.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:55.000][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[2026-03-07 16:02:55.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:55.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:55.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:55.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:55.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:55.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:55.008][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[2026-03-07 16:02:55.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:55.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:55.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:55.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:55.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:55.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:55.015][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[2026-03-07 16:02:55.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:55.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:55.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:55.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:55.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:55.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:55.023][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[2026-03-07 16:02:55.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:55.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:55.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:55.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:55.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:55.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:55.031][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[2026-03-07 16:02:55.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:55.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:55.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:55.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:55.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:55.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:55.039][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[2026-03-07 16:02:55.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:55.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:55.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:55.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:55.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:55.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:55.047][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[2026-03-07 16:02:55.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:55.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:55.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:55.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:55.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:55.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:55.054][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[2026-03-07 16:02:55.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:55.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:55.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:55.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:55.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:55.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:55.062][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[2026-03-07 16:02:55.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:55.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:55.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:55.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:55.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:55.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:55.070][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[2026-03-07 16:02:55.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:55.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:55.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:55.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:55.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:55.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:55.078][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[2026-03-07 16:02:55.081][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-03-07 16:02:55.087][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-03-07 16:02:55.089][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.091][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-03-07 16:02:55.092][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.093][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:55.094][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.096][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:55.097][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.098][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:55.099][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-03-07 16:02:55.101][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:55.102][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.103][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-03-07 16:02:55.104][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:55.105][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-03-07 16:02:55.105][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-03-07 16:02:55.107][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:55.108][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:55.109][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-07 16:02:55.110][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:55.112][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:55.113][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:55.114][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:55.115][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:55.116][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:55.118][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-03-07 16:02:55.118][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-03-07 16:02:55.119][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:55.120][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:55.121][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.122][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:55.124][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-03-07 16:02:55.126][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.128][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-03-07 16:02:55.129][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.130][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:55.131][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.133][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:55.134][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.136][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:55.138][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-07 16:02:55.139][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:55.140][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.142][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-03-07 16:02:55.144][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:55.147][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-03-07 16:02:55.147][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-03-07 16:02:55.147][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-03-07 16:02:55.147][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-03-07 16:02:55.147][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-03-07 16:02:55.147][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-03-07 16:02:55.150][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:55.152][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:55.155][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-07 16:02:55.157][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:55.159][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:55.161][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:55.163][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:55.166][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:55.169][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:55.171][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:55.171][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-07 16:02:55.174][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:55.177][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:55.179][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.182][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:55.185][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-03-07 16:02:55.190][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:55.192][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-03-07 16:02:55.195][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.197][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:55.200][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.202][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:55.204][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.207][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:55.210][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-07 16:02:55.213][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:55.216][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.218][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-03-07 16:02:55.221][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:55.223][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-03-07 16:02:55.223][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:55.223][self$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[2026-03-07 16:02:55.223][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:55.223][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:55.223][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:55.223][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:55.223][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:55.223][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:55.223][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:55.223][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-03-07 16:02:55.223][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:55.223][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:55.223][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:55.227][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:55.229][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:55.229][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:02:55.229][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:02:55.231][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-03-07 16:02:55.233][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:55.235][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:55.237][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:55.240][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:55.242][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:55.245][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:55.247][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:55.247][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-07 16:02:55.247][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-03-07 16:02:55.249][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:55.251][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:55.253][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.256][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-03-07 16:02:55.259][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-03-07 16:02:55.263][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.266][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-03-07 16:02:55.267][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.269][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:55.270][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.272][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:55.274][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.276][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:55.279][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-07 16:02:55.281][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:55.283][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.285][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-03-07 16:02:55.286][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:55.288][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-03-07 16:02:55.288][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-03-07 16:02:55.290][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:55.291][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:55.292][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-03-07 16:02:55.294][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:55.295][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:55.296][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:55.297][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:55.298][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:55.300][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:55.302][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:55.302][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-07 16:02:55.302][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-03-07 16:02:55.304][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:55.306][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:55.308][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:55.310][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-03-07 16:02:55.312][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-03-07 16:02:55.314][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-07 16:02:55.315][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-07 16:02:55.317][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-03-07 16:02:55.319][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-07 16:02:55.321][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-03-07 16:02:55.329][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2026-03-07 16:02:55.334][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2026-03-07 16:02:55.344][biodb::testThat]
biodb.INFO [2026-03-07 16:02:55.346][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-03-07 16:02:55.347][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:55.348][biodb::testThat]
biodb.TRACE[2026-03-07 16:02:55.351][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2026-03-07 16:02:55.353][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2026-03-07 16:02:55.356][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2026-03-07 16:02:55.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-07 16:02:55.360][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:55.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:55.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:55.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:55.369][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:55.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-07 16:02:55.376][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.378][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.379][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.380][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.387][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:55.388][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:55.390][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.391][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.393][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:55.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:55.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.398][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:55.399][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:55.400][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.402][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.403][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:55.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:55.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.408][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:55.410][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:55.411][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.412][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.414][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:55.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:55.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.419][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:55.420][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:55.421][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.423][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.424][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:55.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:55.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.430][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:55.431][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:55.432][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.433][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.435][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:55.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:55.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.440][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-03-07 16:02:55.441][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:55.443][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.444][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.445][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-03-07 16:02:55.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:55.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.451][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:55.452][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:55.453][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.454][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.456][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:55.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:55.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.461][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:55.463][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:55.464][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.465][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.467][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:55.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:55.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.472][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:55.473][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:55.474][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.476][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:55.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:55.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.482][ef$get] Asked field names are: logp.
biodb.TRACE[2026-03-07 16:02:55.484][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-07 16:02:55.485][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.486][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.488][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-07 16:02:55.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-07 16:02:55.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.493][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-03-07 16:02:55.495][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:55.496][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.497][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-03-07 16:02:55.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:55.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.504][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:55.505][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:55.506][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.508][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.509][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:55.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:55.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.515][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:55.516][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:55.517][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.519][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.520][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:55.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:55.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.530][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2026-03-07 16:02:55.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:55.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.535][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:55.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:55.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.540][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:55.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:55.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.545][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2026-03-07 16:02:55.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:55.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.550][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:55.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:55.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.556][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:55.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:55.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.561][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2026-03-07 16:02:55.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:55.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.566][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:55.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:55.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.571][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:55.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:55.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.576][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2026-03-07 16:02:55.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:55.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.581][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:55.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:55.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.586][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:55.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:55.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.591][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2026-03-07 16:02:55.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:55.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.596][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:55.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:55.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.601][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:55.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:55.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.606][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:55.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:55.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.612][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:55.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:55.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.617][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:55.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:55.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.626][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:55.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:55.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-07 16:02:55.661][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2026-03-07 16:02:55.664][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-07 16:02:55.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:55.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.669][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-07 16:02:55.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:55.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.674][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:55.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:55.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.679][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-07 16:02:55.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-07 16:02:55.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.684][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-07 16:02:55.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-07 16:02:55.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.689][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-07 16:02:55.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-07 16:02:55.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.694][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-07 16:02:55.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-07 16:02:55.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.734][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:55.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:55.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.777][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:55.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:55.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.782][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:55.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:55.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.787][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:55.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:55.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.815][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.817][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.818][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.819][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:55.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:55.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.836][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-03-07 16:02:55.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:55.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:55.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:55.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:55.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:55.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.851][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-03-07 16:02:55.853][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:55.854][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.855][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.856][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-03-07 16:02:55.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:55.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-03-07 16:02:55.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:55.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:55.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:55.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:55.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:55.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.888][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-03-07 16:02:55.889][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:55.890][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.891][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.893][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-03-07 16:02:55.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:55.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.928][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:55.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:55.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.937][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:55.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:55.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.946][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:55.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:55.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.955][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:55.957][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:55.959][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.961][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.963][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:55.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:55.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:55.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:55.993][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-07 16:02:55.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-07 16:02:55.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.003][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-07 16:02:56.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-07 16:02:56.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.013][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-07 16:02:56.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-07 16:02:56.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.024][ef$get] Asked field names are: logp.
biodb.TRACE[2026-03-07 16:02:56.026][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-07 16:02:56.028][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.032][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.034][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-07 16:02:56.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-07 16:02:56.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.065][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:56.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:56.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.073][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:56.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:56.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.082][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:56.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:56.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.092][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:56.094][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:56.096][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.098][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.100][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:56.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:56.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.128][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:56.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:56.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.139][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:56.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:56.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.149][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:56.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:56.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.158][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:56.160][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:56.163][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.165][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.168][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:56.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:56.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.196][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.205][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.215][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.224][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.227][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.229][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.232][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.234][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.273][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.283][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.293][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.302][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.305][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.308][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.310][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.313][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.342][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.349][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.354][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.360][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.362][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.363][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.364][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.366][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.387][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.392][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.397][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.402][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.404][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.405][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.406][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.408][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.424][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.429][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.435][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.440][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.441][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.442][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.444][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.445][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.462][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:56.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:56.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.467][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:56.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:56.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.472][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:56.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:56.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.477][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:56.479][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:56.480][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.481][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.482][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:56.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:56.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.505][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:56.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:56.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.511][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:56.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:56.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.516][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:56.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:56.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.522][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:56.523][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:56.524][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.526][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.527][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:56.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:56.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:56.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:56.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:56.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:56.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.554][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:56.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:56.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.559][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:56.560][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:56.562][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.563][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.564][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:56.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:56.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.580][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:56.581][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:56.582][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.584][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.590][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.591][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.593][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.594][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.600][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.602][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.603][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.604][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.610][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.612][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.613][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.614][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.621][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.622][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.624][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.625][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.631][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.633][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.634][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.635][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.642][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:56.643][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:56.644][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.646][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.652][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:56.654][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:56.655][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.656][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.663][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:56.664][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:56.666][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.667][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.673][ef$get] Asked field names are: logp.
biodb.TRACE[2026-03-07 16:02:56.675][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-07 16:02:56.676][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.677][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.684][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:56.686][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:56.687][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.688][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.699][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:56.701][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:56.702][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.703][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.710][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:56.712][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:56.713][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.714][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.720][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:56.722][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:56.723][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.724][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.730][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:56.732][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:56.733][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.734][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.741][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2026-03-07 16:02:56.743][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2026-03-07 16:02:56.744][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2026-03-07 16:02:56.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-07 16:02:56.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:56.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:56.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:56.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:56.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:56.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-07 16:02:56.762][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:56.763][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:56.764][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.765][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:56.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:56.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.772][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.774][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.775][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.776][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.778][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.783][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.784][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.785][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.786][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.788][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.793][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.794][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.796][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.797][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.798][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.804][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.805][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.806][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.807][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.809][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.814][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.815][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.817][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.818][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.819][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.825][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-03-07 16:02:56.826][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:56.827][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.828][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.830][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-03-07 16:02:56.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:56.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.835][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:56.836][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:56.838][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.839][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.841][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:56.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:56.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.846][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:56.847][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:56.848][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.849][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:56.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:56.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.856][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:56.858][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:56.859][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.860][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.862][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:56.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:56.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.867][ef$get] Asked field names are: logp.
biodb.TRACE[2026-03-07 16:02:56.869][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-07 16:02:56.870][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.871][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.873][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-07 16:02:56.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-07 16:02:56.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.878][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-03-07 16:02:56.880][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:56.881][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.882][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-03-07 16:02:56.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:56.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.895][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:56.896][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:56.897][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.898][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.900][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:56.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:56.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.905][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:56.907][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:56.908][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.909][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.911][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:56.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:56.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.916][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2026-03-07 16:02:56.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.922][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.927][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:56.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.932][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2026-03-07 16:02:56.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.937][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.942][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:56.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.947][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2026-03-07 16:02:56.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.952][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.957][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:56.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.962][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2026-03-07 16:02:56.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.967][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.972][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:56.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.977][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2026-03-07 16:02:56.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.983][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.988][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:56.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.993][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:56.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:56.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:56.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:56.998][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:56.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:57.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.003][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:57.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:57.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.013][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:57.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:57.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-07 16:02:57.048][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2026-03-07 16:02:57.051][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-07 16:02:57.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:57.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.056][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-07 16:02:57.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:02:57.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.061][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:57.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:02:57.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.070][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-07 16:02:57.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-07 16:02:57.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.076][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-07 16:02:57.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-07 16:02:57.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.081][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-07 16:02:57.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-07 16:02:57.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.086][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-07 16:02:57.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-07 16:02:57.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.103][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:57.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:57.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.147][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:57.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:57.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.152][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:57.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:57.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.157][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:57.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:57.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.186][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.187][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.188][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.189][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:57.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:57.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:57.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:57.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:57.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:57.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.222][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:57.224][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:57.225][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.226][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:57.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:57.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.244][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:57.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:57.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.250][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:57.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:57.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:57.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:57.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.266][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:57.268][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:57.269][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.270][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:57.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:57.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.289][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:57.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:57.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.296][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:57.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:57.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.302][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:57.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:57.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.307][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:57.309][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:57.310][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.312][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.313][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:57.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:57.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.330][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-07 16:02:57.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-07 16:02:57.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.336][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-07 16:02:57.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-07 16:02:57.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.341][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-07 16:02:57.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-07 16:02:57.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.347][ef$get] Asked field names are: logp.
biodb.TRACE[2026-03-07 16:02:57.348][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-07 16:02:57.349][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.350][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.352][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-07 16:02:57.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-07 16:02:57.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.368][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:57.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:57.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.373][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:57.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:57.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.378][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:57.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:57.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.383][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:57.385][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:57.386][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.387][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.388][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:57.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:57.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.404][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:57.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:57.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.410][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:57.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:57.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.415][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:57.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:57.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.420][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:57.422][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:57.423][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.424][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.425][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:57.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:57.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.442][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:57.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:57.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.448][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:57.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:57.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.458][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:57.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:57.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.464][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:57.465][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:57.466][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.468][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.469][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:57.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:57.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.485][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:57.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:57.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.490][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:57.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:57.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.495][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:57.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:57.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.500][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:57.502][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:57.503][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.504][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.505][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:57.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:57.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.521][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:57.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:57.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.526][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:57.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:57.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.531][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:57.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:57.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.537][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:57.538][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:57.539][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.541][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.542][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:57.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:57.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.558][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:57.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:57.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.564][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:57.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:57.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.569][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:57.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:57.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.574][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:57.576][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:57.577][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.578][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.579][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:57.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:57.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.595][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:57.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:57.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.600][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:57.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:57.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.605][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:57.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:57.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.610][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:57.611][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:57.613][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.614][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.615][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:57.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:57.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.630][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:57.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:57.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.635][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:57.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:57.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.645][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:57.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:57.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.651][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:57.652][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:57.653][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.654][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.656][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:57.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:57.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.672][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:57.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:57.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.677][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:57.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:57.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.682][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:57.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:57.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.687][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:57.688][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:57.689][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.690][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.692][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:57.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:57.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.707][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:57.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:57.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.712][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:57.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:57.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.718][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:57.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:57.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.723][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:57.724][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:57.726][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.727][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.728][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:57.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:57.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.744][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:57.746][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:57.747][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.748][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.755][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:57.756][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-07 16:02:57.758][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.759][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.765][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:57.767][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-07 16:02:57.768][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.769][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.776][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:57.777][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-07 16:02:57.779][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.780][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.786][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:57.788][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:57.789][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.790][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.797][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:57.798][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:57.800][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.801][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.807][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:57.809][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:57.810][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.811][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.818][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:57.819][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:57.820][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.822][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.828][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:57.830][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:57.836][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.837][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.844][ef$get] Asked field names are: logp.
biodb.TRACE[2026-03-07 16:02:57.845][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-07 16:02:57.847][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.848][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.854][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:57.855][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:57.857][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.858][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.864][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:57.866][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:57.867][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.868][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.874][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:57.876][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:57.877][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.878][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.884][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:57.886][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-07 16:02:57.887][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.888][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:57.894][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:57.896][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-07 16:02:57.897][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.898][ef$get] fields variable is a list.
biodb.INFO [2026-03-07 16:02:57.909][biodb::testThat]
biodb.INFO [2026-03-07 16:02:57.910][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-03-07 16:02:57.911][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:57.912][biodb::testThat]
biodb.DEBUG[2026-03-07 16:02:57.915][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-03-07 16:02:57.920][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-03-07 16:02:57.922][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-07 16:02:57.923][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:02:57.925][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:57.926][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:02:57.927][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-07 16:02:57.929][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-07 16:02:57.986][biodb::testThat]
biodb.INFO [2026-03-07 16:02:57.987][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-03-07 16:02:57.989][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:57.990][biodb::testThat]
biodb.TRACE[2026-03-07 16:02:57.994][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:57.995][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:57.997][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:57.998][ef$get] fields variable is a list.
biodb.DEBUG[2026-03-07 16:02:57.999][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2026-03-07 16:02:58.011][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-03-07 16:02:58.012][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-03-07 16:02:58.019][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-07 16:02:58.020][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:02:58.022][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:58.023][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:02:58.024][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-07 16:02:58.026][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-07 16:02:58.083][biodb::testThat]
biodb.INFO [2026-03-07 16:02:58.085][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-03-07 16:02:58.086][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:58.087][biodb::testThat]
biodb.DEBUG[2026-03-07 16:02:58.097][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-03-07 16:02:58.098][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-03-07 16:02:58.100][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-07 16:02:58.101][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:02:58.103][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:58.104][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:02:58.105][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-07 16:02:58.107][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-07 16:02:58.165][biodb::testThat]
biodb.INFO [2026-03-07 16:02:58.167][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-03-07 16:02:58.168][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:58.169][biodb::testThat]
biodb.DEBUG[2026-03-07 16:02:58.174][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-03-07 16:02:58.176][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-03-07 16:02:58.177][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-07 16:02:58.179][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:02:58.185][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:58.187][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:02:58.188][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-07 16:02:58.189][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-07 16:02:58.248][biodb::testThat]
biodb.INFO [2026-03-07 16:02:58.249][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-03-07 16:02:58.250][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:58.251][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-07 16:02:58.310][biodb::testThat]
biodb.INFO [2026-03-07 16:02:58.311][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-03-07 16:02:58.312][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:58.314][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-07 16:02:58.377][biodb::testThat]
biodb.INFO [2026-03-07 16:02:58.379][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-03-07 16:02:58.380][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:58.381][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-07 16:02:58.440][biodb::testThat]
biodb.INFO [2026-03-07 16:02:58.442][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-03-07 16:02:58.443][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:58.444][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2026-03-07 16:02:58.517][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:58.519][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:58.520][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:58.521][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:58.522][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:58.524][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:58.525][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:58.526][ef$get] fields variable is a list.
biodb.INFO [2026-03-07 16:02:58.528][biodb::testThat]
biodb.INFO [2026-03-07 16:02:58.530][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2026-03-07 16:02:58.531][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:58.532][biodb::testThat]
biodb.DEBUG[2026-03-07 16:02:58.541][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-03-07 16:02:58.543][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-03-07 16:02:58.545][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-07 16:02:58.546][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:02:58.547][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:58.549][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:02:58.550][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-07 16:02:58.551][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-07 16:02:58.610][biodb::testThat]
biodb.INFO [2026-03-07 16:02:58.611][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2026-03-07 16:02:58.613][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:58.614][biodb::testThat]
biodb.DEBUG[2026-03-07 16:02:58.618][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-03-07 16:02:58.619][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-03-07 16:02:58.621][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-07 16:02:58.622][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:02:58.623][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:58.625][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:02:58.626][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-07 16:02:58.627][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-07 16:02:58.693][biodb::testThat]
biodb.INFO [2026-03-07 16:02:58.694][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2026-03-07 16:02:58.696][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:58.697][biodb::testThat]
biodb.DEBUG[2026-03-07 16:02:58.701][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-03-07 16:02:58.702][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-03-07 16:02:58.704][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-07 16:02:58.706][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:02:58.707][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:58.709][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:02:58.710][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-07 16:02:58.711][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-07 16:02:58.770][biodb::testThat]
biodb.INFO [2026-03-07 16:02:58.772][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2026-03-07 16:02:58.773][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:58.774][biodb::testThat]
biodb.DEBUG[2026-03-07 16:02:58.778][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-03-07 16:02:58.779][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-03-07 16:02:58.781][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-07 16:02:58.783][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:02:58.784][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:58.785][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:02:58.786][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-07 16:02:58.788][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2026-03-07 16:02:58.852][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:58.853][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:58.855][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:58.856][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:58.857][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:58.858][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:02:58.860][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:58.861][ef$get] fields variable is a list.
biodb.INFO [2026-03-07 16:02:58.863][biodb::testThat]
biodb.INFO [2026-03-07 16:02:58.864][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2026-03-07 16:02:58.865][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:58.867][biodb::testThat]
biodb.DEBUG[2026-03-07 16:02:58.870][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-03-07 16:02:58.872][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-03-07 16:02:58.874][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-07 16:02:58.875][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:02:58.876][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:58.878][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:02:58.879][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-07 16:02:58.880][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-07 16:02:58.939][biodb::testThat]
biodb.INFO [2026-03-07 16:02:58.940][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2026-03-07 16:02:58.941][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:58.943][biodb::testThat]
biodb.DEBUG[2026-03-07 16:02:58.947][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-03-07 16:02:58.948][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-03-07 16:02:58.950][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-07 16:02:58.951][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:02:58.953][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:58.954][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:02:58.955][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-07 16:02:58.957][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-07 16:02:59.021][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-07 16:02:59.023][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2026-03-07 16:02:59.024][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-07 16:02:59.025][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:59.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:59.028][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.030][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-03-07 16:02:59.037][biodb::testContext]
biodb.INFO [2026-03-07 16:02:59.038][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-07 16:02:59.039][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2026-03-07 16:02:59.040][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-07 16:02:59.041][biodb::testContext]
biodb.INFO [2026-03-07 16:02:59.044][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-07 16:02:59.046][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-03-07 16:02:59.050][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:02:59.052][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-07 16:02:59.053][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-07 16:02:59.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.056][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[2026-03-07 16:02:59.058][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-07 16:02:59.059][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-07 16:02:59.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:59.064][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-07 16:02:59.065][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-07 16:02:59.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.069][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[2026-03-07 16:02:59.070][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-07 16:02:59.071][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-07 16:02:59.073][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-07 16:02:59.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:59.077][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-07 16:02:59.079][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-07 16:02:59.080][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-07 16:02:59.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.083][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[2026-03-07 16:02:59.085][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-07 16:02:59.086][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-07 16:02:59.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:59.091][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-07 16:02:59.092][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-07 16:02:59.093][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-07 16:02:59.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.097][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[2026-03-07 16:02:59.098][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-07 16:02:59.100][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-07 16:02:59.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:59.104][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-07 16:02:59.106][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-07 16:02:59.107][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-07 16:02:59.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.111][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[2026-03-07 16:02:59.112][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-07 16:02:59.113][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-07 16:02:59.115][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-07 16:02:59.116][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-07 16:02:59.117][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-07 16:02:59.118][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-07 16:02:59.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:59.123][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-07 16:02:59.124][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-07 16:02:59.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.128][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[2026-03-07 16:02:59.129][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-07 16:02:59.131][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-07 16:02:59.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:59.135][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-07 16:02:59.137][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-07 16:02:59.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.140][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[2026-03-07 16:02:59.142][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-07 16:02:59.143][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-07 16:02:59.144][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-07 16:02:59.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:59.149][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-07 16:02:59.150][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-07 16:02:59.161][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-07 16:02:59.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.165][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[2026-03-07 16:02:59.166][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-07 16:02:59.167][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-07 16:02:59.169][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-07 16:02:59.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:59.173][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-07 16:02:59.176][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:59.182][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-03-07 16:02:59.183][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.185][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:59.186][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.188][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.189][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:59.190][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.191][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-07 16:02:59.193][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:59.194][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.195][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-07 16:02:59.197][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:59.198][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:59.199][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.200][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:59.200][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:02:59.200][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:02:59.200][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-07 16:02:59.200][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-07 16:02:59.202][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:59.203][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:59.204][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:59.205][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:59.207][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:59.208][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:59.209][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.210][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:59.212][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:59.213][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:59.214][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:59.215][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:59.217][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-07 16:02:59.219][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:59.220][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-07 16:02:59.222][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.223][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:59.224][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.225][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.227][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:59.228][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.229][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-07 16:02:59.230][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:59.232][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.233][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-07 16:02:59.234][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:59.236][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:59.237][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.238][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:59.238][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:02:59.238][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:02:59.238][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-07 16:02:59.238][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-07 16:02:59.240][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:59.241][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:59.242][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:59.243][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:59.245][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:59.246][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:59.247][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.248][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:59.250][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:59.251][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:59.252][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:59.253][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:59.255][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-07 16:02:59.257][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.258][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-03-07 16:02:59.260][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.261][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:59.262][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.263][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.265][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:59.266][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.267][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-07 16:02:59.268][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:59.270][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:59.271][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-07 16:02:59.272][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:59.274][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:59.275][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.276][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:59.277][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:59.279][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:59.280][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:59.281][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:59.282][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:59.283][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:59.285][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.286][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:59.287][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:59.288][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:59.290][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:59.291][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:59.292][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-07 16:02:59.294][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.296][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-07 16:02:59.297][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.298][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:59.300][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.301][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.302][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:59.303][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.305][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-07 16:02:59.306][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:59.307][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:59.308][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-07 16:02:59.310][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:59.311][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:59.312][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.314][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:59.315][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:59.316][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:59.317][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:59.318][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:59.320][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:59.321][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:59.322][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.323][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:59.324][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:59.326][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:59.327][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:59.328][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:59.330][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:02:59.331][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.332][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[2026-03-07 16:02:59.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.338][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[2026-03-07 16:02:59.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.343][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[2026-03-07 16:02:59.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.349][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[2026-03-07 16:02:59.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.360][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[2026-03-07 16:02:59.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.365][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[2026-03-07 16:02:59.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.371][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[2026-03-07 16:02:59.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.376][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[2026-03-07 16:02:59.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.382][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[2026-03-07 16:02:59.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.387][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[2026-03-07 16:02:59.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.393][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[2026-03-07 16:02:59.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.399][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[2026-03-07 16:02:59.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.404][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[2026-03-07 16:02:59.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.410][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[2026-03-07 16:02:59.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.416][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[2026-03-07 16:02:59.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.421][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[2026-03-07 16:02:59.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.427][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[2026-03-07 16:02:59.428][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-07 16:02:59.430][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-07 16:02:59.432][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-07 16:02:59.434][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-07 16:02:59.435][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-07 16:02:59.437][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-07 16:02:59.439][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-07 16:02:59.441][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-07 16:02:59.443][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-07 16:02:59.445][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-07 16:02:59.446][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-07 16:02:59.448][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-07 16:02:59.450][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-07 16:02:59.452][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-07 16:02:59.454][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-07 16:02:59.455][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-07 16:02:59.457][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-07 16:02:59.459][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-07 16:02:59.461][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-07 16:02:59.463][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-07 16:02:59.465][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-07 16:02:59.466][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-07 16:02:59.468][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-07 16:02:59.470][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-07 16:02:59.472][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-07 16:02:59.474][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-07 16:02:59.476][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-07 16:02:59.478][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-07 16:02:59.480][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-07 16:02:59.482][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-07 16:02:59.484][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-07 16:02:59.486][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-07 16:02:59.488][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-07 16:02:59.491][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-07 16:02:59.493][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-07 16:02:59.495][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-07 16:02:59.497][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-07 16:02:59.500][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-07 16:02:59.502][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-07 16:02:59.504][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-07 16:02:59.507][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-07 16:02:59.509][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-07 16:02:59.511][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-07 16:02:59.513][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-07 16:02:59.516][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-07 16:02:59.518][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-07 16:02:59.520][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-07 16:02:59.522][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-07 16:02:59.524][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-07 16:02:59.527][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-07 16:02:59.534][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-07 16:02:59.536][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-07 16:02:59.539][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-07 16:02:59.541][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-07 16:02:59.543][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-07 16:02:59.546][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-07 16:02:59.548][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-07 16:02:59.550][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-07 16:02:59.552][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-07 16:02:59.556][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-07 16:02:59.559][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-07 16:02:59.563][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-07 16:02:59.565][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-07 16:02:59.568][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-07 16:02:59.570][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-07 16:02:59.572][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-07 16:02:59.574][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-07 16:02:59.579][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-07 16:02:59.581][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-07 16:02:59.589][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-07 16:02:59.592][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-07 16:02:59.594][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-07 16:02:59.596][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-07 16:02:59.598][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-07 16:02:59.600][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-07 16:02:59.648][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-07 16:02:59.650][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-07 16:02:59.652][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-07 16:02:59.654][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-07 16:02:59.656][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-07 16:02:59.657][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-07 16:02:59.709][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-07 16:02:59.711][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-07 16:02:59.713][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-07 16:02:59.715][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-07 16:02:59.726][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:02:59.727][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.729][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.731][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[2026-03-07 16:02:59.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:59.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:59.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.754][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[2026-03-07 16:02:59.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:59.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:59.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.762][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[2026-03-07 16:02:59.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:59.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:59.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.770][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[2026-03-07 16:02:59.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:59.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:59.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.778][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[2026-03-07 16:02:59.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:59.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:59.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.785][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[2026-03-07 16:02:59.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:59.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:59.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.793][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[2026-03-07 16:02:59.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:59.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:59.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.801][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[2026-03-07 16:02:59.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:59.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:59.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.809][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[2026-03-07 16:02:59.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:59.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:59.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.817][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[2026-03-07 16:02:59.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:59.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:59.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.825][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[2026-03-07 16:02:59.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:59.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:59.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.833][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[2026-03-07 16:02:59.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:59.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:59.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.841][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[2026-03-07 16:02:59.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:59.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:59.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.857][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[2026-03-07 16:02:59.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:59.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:59.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.866][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[2026-03-07 16:02:59.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:59.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:59.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.873][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[2026-03-07 16:02:59.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:59.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:59.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:59.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:59.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:59.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:59.881][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[2026-03-07 16:02:59.884][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-03-07 16:02:59.886][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-03-07 16:02:59.888][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.890][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-03-07 16:02:59.891][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.892][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:59.893][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.895][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.896][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.897][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.898][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-03-07 16:02:59.900][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:59.901][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.902][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-03-07 16:02:59.903][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:59.905][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-03-07 16:02:59.905][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-03-07 16:02:59.906][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:59.907][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:59.909][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-07 16:02:59.910][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:59.911][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:59.912][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:59.913][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:59.914][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:59.916][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.917][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-03-07 16:02:59.917][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-03-07 16:02:59.918][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:59.919][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:59.921][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.922][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:59.923][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-03-07 16:02:59.926][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.927][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-03-07 16:02:59.928][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.930][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:59.931][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.932][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.934][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.935][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.936][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-07 16:02:59.937][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:59.939][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.940][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-03-07 16:02:59.941][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:59.942][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-03-07 16:02:59.942][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-03-07 16:02:59.942][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-03-07 16:02:59.942][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-03-07 16:02:59.942][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-03-07 16:02:59.942][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-03-07 16:02:59.944][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:59.945][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:59.946][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-07 16:02:59.948][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:59.949][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:59.950][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:59.951][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:59.952][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:59.954][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.955][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:59.955][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-07 16:02:59.956][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:59.957][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:59.959][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.960][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:59.961][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-03-07 16:02:59.964][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:59.965][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-03-07 16:02:59.966][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.968][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:59.969][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.970][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.971][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.973][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.974][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-07 16:02:59.975][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:59.977][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.978][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-03-07 16:02:59.979][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:59.981][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-03-07 16:02:59.981][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:59.981][self$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[2026-03-07 16:02:59.981][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:59.981][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:59.981][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:59.981][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:59.981][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:59.981][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:59.981][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:59.981][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-03-07 16:02:59.981][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:59.981][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:59.981][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-07 16:02:59.982][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:59.984][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:59.984][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:02:59.984][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:02:59.985][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-03-07 16:02:59.986][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:59.987][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:59.989][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:59.990][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:59.991][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:59.992][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:59.994][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:02:59.994][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-07 16:02:59.994][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-03-07 16:02:59.995][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:59.996][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:59.997][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:59.999][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-03-07 16:03:00.000][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-03-07 16:03:00.003][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:00.004][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-03-07 16:03:00.006][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:00.007][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:03:00.008][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:00.009][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:03:00.011][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:00.012][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:03:00.013][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-07 16:03:00.014][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:03:00.016][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:00.017][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-03-07 16:03:00.018][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:03:00.020][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-03-07 16:03:00.020][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-03-07 16:03:00.026][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:00.027][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:00.029][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-03-07 16:03:00.030][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:00.031][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:00.033][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:03:00.034][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:00.036][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:00.037][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:03:00.038][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:03:00.038][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-07 16:03:00.038][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-03-07 16:03:00.039][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:03:00.041][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:03:00.042][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:00.043][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-03-07 16:03:00.045][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-03-07 16:03:00.047][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-07 16:03:00.049][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-07 16:03:00.050][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-03-07 16:03:00.052][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-07 16:03:00.055][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-03-07 16:03:00.061][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2026-03-07 16:03:00.066][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2026-03-07 16:03:00.071][biodb::testThat]
biodb.INFO [2026-03-07 16:03:00.073][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-03-07 16:03:00.074][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:00.075][biodb::testThat]
biodb.TRACE[2026-03-07 16:03:00.079][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2026-03-07 16:03:00.081][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2026-03-07 16:03:00.084][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2026-03-07 16:03:00.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-07 16:03:00.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:00.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:00.095][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:00.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:00.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:00.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-07 16:03:00.102][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.103][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.104][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.106][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.112][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:00.114][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:00.115][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.116][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.118][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:00.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:00.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.123][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-07 16:03:00.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-07 16:03:00.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.128][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-07 16:03:00.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-07 16:03:00.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.138][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-07 16:03:00.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-07 16:03:00.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-07 16:03:00.174][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2026-03-07 16:03:00.177][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-07 16:03:00.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:03:00.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.182][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-07 16:03:00.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-07 16:03:00.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.187][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:03:00.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-07 16:03:00.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.193][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-07 16:03:00.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-07 16:03:00.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.198][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-07 16:03:00.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-07 16:03:00.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.203][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-07 16:03:00.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-07 16:03:00.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.214][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-07 16:03:00.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-07 16:03:00.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.231][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-07 16:03:00.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-07 16:03:00.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.277][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-07 16:03:00.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-07 16:03:00.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.282][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-07 16:03:00.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-07 16:03:00.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.287][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-07 16:03:00.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-07 16:03:00.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.316][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.318][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.319][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.320][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.338][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:00.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:00.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.343][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:00.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:00.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.348][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:00.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:00.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.354][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:00.355][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:00.356][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.358][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.359][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:00.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:00.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.375][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:00.377][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:00.378][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.379][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:00.386][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:00.388][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:00.389][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:00.396][ef$get] fields variable is a list.
biodb.INFO [2026-03-07 16:03:00.408][biodb::testThat]
biodb.INFO [2026-03-07 16:03:00.410][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-03-07 16:03:00.411][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:00.413][biodb::testThat]
biodb.DEBUG[2026-03-07 16:03:00.416][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2026-03-07 16:03:00.421][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2026-03-07 16:03:00.423][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-07 16:03:00.425][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:03:00.426][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:03:00.428][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:03:00.429][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-07 16:03:00.430][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-03-07 16:03:00.489][biodb::testThat]
biodb.INFO [2026-03-07 16:03:00.491][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-03-07 16:03:00.492][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:00.493][biodb::testThat]
biodb.INFO [2026-03-07 16:03:00.501][biodb::testThat]
biodb.INFO [2026-03-07 16:03:00.502][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-03-07 16:03:00.504][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:00.505][biodb::testThat]
biodb.WARN [2026-03-07 16:03:00.508][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-03-07 16:03:00.513][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-03-07 16:03:00.524][biodb::testThat]
biodb.INFO [2026-03-07 16:03:00.526][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-03-07 16:03:00.527][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:00.528][biodb::testThat]
biodb.DEBUG[2026-03-07 16:03:00.534][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2026-03-07 16:03:00.535][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2026-03-07 16:03:00.537][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-07 16:03:00.539][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2026-03-07 16:03:00.541][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-07 16:03:00.542][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-07 16:03:00.544][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-07 16:03:00.545][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-03-07 16:03:00.613][biodb::testThat]
biodb.INFO [2026-03-07 16:03:00.614][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-03-07 16:03:00.616][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:00.617][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-03-07 16:03:00.678][biodb::testThat]
biodb.INFO [2026-03-07 16:03:00.679][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-03-07 16:03:00.680][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:00.682][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-03-07 16:03:00.745][biodb::testThat]
biodb.INFO [2026-03-07 16:03:00.747][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-03-07 16:03:00.748][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:00.749][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-03-07 16:03:00.808][biodb::testThat]
biodb.INFO [2026-03-07 16:03:00.809][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-03-07 16:03:00.810][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:00.811][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-03-07 16:03:00.869][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-07 16:03:00.871][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2026-03-07 16:03:00.872][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-07 16:03:00.873][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:00.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:00.875][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:00.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:00.882][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:00.883][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 31 | WARN 1 | SKIP 1 | PASS 247 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1):

══ 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$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
  3.   └─conn$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_400_pubchem.subst.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 = `<NcbPbcSC>`, 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_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 31 | WARN 1 | SKIP 1 | PASS 247 ]
Error:
! Test failures.
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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.14.0’
* 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’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  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 31 | WARN 1 | SKIP 1 | PASS 247 ]
  Error:
  ! Test failures.
  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, 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 ‘1.14.0’
** 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)