Long Tests report for BioC 3.22 - CHECK results for biodbNcbi on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4882
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4673
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*

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: 2025-12-13 16:01:59 -0500 (Sat, 13 Dec 2025)

EndedAt: 2025-12-13 16:03:11 -0500 (Sat, 13 Dec 2025)

EllapsedTime: 71.6 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 [2025-12-13 16:02:57.880][biodb::testContext]
biodb.INFO [2025-12-13 16:02:57.884][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-13 16:02:57.885][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2025-12-13 16:02:57.886][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-13 16:02:57.888][biodb::testContext]
biodb.INFO [2025-12-13 16:02:57.895][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-13 16:02:57.897][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-12-13 16:02:57.905][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:02:57.906][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-13 16:02:57.908][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-13 16:02:57.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:57.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:57.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:57.913][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-13 16:02:57.938][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-13 16:02:57.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:57.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:57.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:57.952][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-13 16:02:57.953][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-13 16:02:57.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:57.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:57.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:57.958][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-13 16:02:57.959][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-13 16:02:57.960][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-13 16:02:57.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:57.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:57.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:57.965][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-13 16:02:57.966][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-13 16:02:57.967][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-13 16:02:57.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:57.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:57.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:57.972][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-13 16:02:57.973][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-13 16:02:57.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:57.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:57.976][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[2025-12-13 16:02:57.977][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-13 16:02:57.979][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-13 16:02:57.980][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-13 16:02:57.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:57.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:57.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:57.984][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-13 16:02:57.986][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-13 16:02:57.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:57.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:57.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:57.990][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-13 16:02:57.991][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-13 16:02:57.993][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-13 16:02:57.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:57.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:57.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:57.997][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-13 16:02:57.998][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-13 16:02:58.000][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-13 16:02:58.001][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-13 16:02:58.002][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-13 16:02:58.003][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-13 16:02:58.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.008][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-13 16:02:58.009][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-13 16:02:58.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.013][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-13 16:02:58.014][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-13 16:02:58.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.019][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-13 16:02:58.020][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-13 16:02:58.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.025][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-13 16:02:58.026][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-13 16:02:58.027][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-13 16:02:58.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.031][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-13 16:02:58.033][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-13 16:02:58.043][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-13 16:02:58.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.047][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-13 16:02:58.049][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-13 16:02:58.050][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-13 16:02:58.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.057][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-13 16:02:58.098][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:58.119][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-13 16:02:58.121][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.122][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:02:58.123][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.124][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.126][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:58.127][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.128][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-13 16:02:58.129][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:02:58.131][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.132][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-13 16:02:58.133][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:02:58.134][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:58.135][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.137][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:02:58.137][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:02:58.137][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:02:58.137][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-13 16:02:58.137][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-13 16:02:58.138][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:02:58.139][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:58.140][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:58.142][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:02:58.143][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:58.144][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:58.145][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.146][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:58.147][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:02:58.149][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:02:58.150][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:58.151][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:58.152][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-13 16:02:58.155][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:58.156][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-13 16:02:58.157][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.158][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:02:58.159][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.165][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.166][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:58.168][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.169][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-13 16:02:58.170][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:02:58.171][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.173][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-13 16:02:58.174][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:02:58.175][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:58.176][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.177][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:02:58.177][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:02:58.177][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:02:58.177][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-13 16:02:58.177][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-13 16:02:58.179][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:02:58.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:58.181][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:58.182][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:02:58.183][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:58.184][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:58.186][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.187][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:58.188][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:02:58.189][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:02:58.190][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:58.191][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:58.193][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-13 16:02:58.195][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.196][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-13 16:02:58.197][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.199][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:02:58.200][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.201][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.202][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:58.203][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.205][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-13 16:02:58.206][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:02:58.207][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:58.208][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-13 16:02:58.210][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:02:58.211][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:58.212][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.213][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:58.214][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:02:58.216][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:58.217][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:58.218][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:02:58.219][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:58.220][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:58.221][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.222][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:58.224][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:02:58.225][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:02:58.226][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:58.227][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:58.228][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-13 16:02:58.230][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.232][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-13 16:02:58.233][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.234][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:02:58.235][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.237][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.238][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:58.239][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.240][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-13 16:02:58.241][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:02:58.243][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:58.244][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-13 16:02:58.245][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:02:58.246][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:58.247][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.249][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:58.250][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:02:58.251][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:58.252][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:58.253][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:02:58.254][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:58.255][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:58.257][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.258][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:58.259][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:02:58.260][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:02:58.261][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:58.262][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:58.266][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:02:58.268][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.358][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-13 16:02:58.362][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-13 16:02:58.364][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-13 16:02:58.365][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-13 16:02:58.371][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-13 16:02:58.373][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-13 16:02:58.374][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-13 16:02:58.376][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-13 16:02:58.378][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-13 16:02:58.379][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-13 16:02:58.381][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-13 16:02:58.382][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-13 16:02:58.384][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-13 16:02:58.386][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-13 16:02:58.387][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-13 16:02:58.389][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-13 16:02:58.391][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-13 16:02:58.392][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-13 16:02:58.394][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-13 16:02:58.396][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-13 16:02:58.397][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-13 16:02:58.399][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-13 16:02:58.401][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-13 16:02:58.402][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-13 16:02:58.404][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-13 16:02:58.406][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-13 16:02:58.407][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-13 16:02:58.409][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-13 16:02:58.411][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-13 16:02:58.412][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-13 16:02:58.414][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-13 16:02:58.416][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-13 16:02:58.417][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-13 16:02:58.419][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-13 16:02:58.421][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-13 16:02:58.422][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-13 16:02:58.424][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-13 16:02:58.425][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-13 16:02:58.427][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-13 16:02:58.429][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-13 16:02:58.430][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-13 16:02:58.432][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-13 16:02:58.434][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-13 16:02:58.435][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-13 16:02:58.437][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-13 16:02:58.439][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-13 16:02:58.440][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-13 16:02:58.442][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-13 16:02:58.444][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-13 16:02:58.445][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-13 16:02:58.447][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-13 16:02:58.448][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-13 16:02:58.450][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-13 16:02:58.452][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-13 16:02:58.453][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-13 16:02:58.455][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-13 16:02:58.457][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-13 16:02:58.458][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-13 16:02:58.460][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-13 16:02:58.462][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-13 16:02:58.463][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-13 16:02:58.465][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-13 16:02:58.466][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-13 16:02:58.468][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-13 16:02:58.470][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-13 16:02:58.471][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-13 16:02:58.473][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-13 16:02:58.475][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-13 16:02:58.476][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-13 16:02:58.478][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-13 16:02:58.480][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-13 16:02:58.481][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-13 16:02:58.483][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-13 16:02:58.484][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-13 16:02:58.486][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-13 16:02:58.488][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-13 16:02:58.489][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-13 16:02:58.491][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-13 16:02:58.493][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-13 16:02:58.494][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-13 16:02:58.496][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-13 16:02:58.498][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-13 16:02:58.499][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-13 16:02:58.507][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-13 16:02:58.509][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-13 16:02:58.512][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:02:58.513][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.515][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:58.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:58.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:58.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:58.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.536][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[2025-12-13 16:02:58.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:58.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:58.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.544][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[2025-12-13 16:02:58.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:58.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:58.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:58.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:58.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:58.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:58.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:58.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:58.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:58.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:58.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:58.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:58.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:58.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:58.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:58.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:58.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:58.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:58.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:58.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:58.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:58.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:58.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:58.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:58.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:58.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:58.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:58.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:58.651][bdb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-12-13 16:02:58.663][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-12-13 16:02:58.666][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.667][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-12-13 16:02:58.668][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.669][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:02:58.671][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.672][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.673][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.674][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.675][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-12-13 16:02:58.677][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:02:58.678][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.679][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-12-13 16:02:58.680][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:02:58.682][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-12-13 16:02:58.682][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-12-13 16:02:58.683][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:58.684][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:58.685][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-13 16:02:58.686][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:58.687][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:58.689][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:02:58.690][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:58.691][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:58.692][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.693][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-13 16:02:58.693][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-12-13 16:02:58.694][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:02:58.695][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:02:58.697][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.698][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:58.699][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-12-13 16:02:58.702][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.703][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-12-13 16:02:58.704][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.705][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:02:58.706][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.708][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.709][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.710][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.711][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-13 16:02:58.712][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:02:58.714][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.715][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-12-13 16:02:58.716][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:02:58.717][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-12-13 16:02:58.717][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-12-13 16:02:58.717][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-12-13 16:02:58.717][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-12-13 16:02:58.717][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-12-13 16:02:58.717][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-12-13 16:02:58.719][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:58.720][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:02:58.721][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-13 16:02:58.722][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:58.723][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:58.724][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:02:58.725][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:58.726][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:58.728][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.729][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:02:58.729][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-13 16:02:58.730][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:02:58.731][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:02:58.732][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.733][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:58.735][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-12-13 16:02:58.737][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:58.738][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-12-13 16:02:58.740][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.741][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:02:58.742][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.743][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.744][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.746][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.747][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-13 16:02:58.748][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:02:58.749][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.750][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-12-13 16:02:58.752][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:02:58.753][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-13 16:02:58.753][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:02:58.753][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:02:58.753][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:02:58.753][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:02:58.753][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:02:58.753][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:02:58.753][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:02:58.753][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:02:58.753][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:02:58.753][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-12-13 16:02:58.753][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:02:58.753][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:02:58.753][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:02:58.758][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:58.759][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:02:58.759][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:02:58.759][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:02:58.760][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-13 16:02:58.761][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:58.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:58.764][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:02:58.765][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:58.766][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:58.767][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.768][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:02:58.768][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-13 16:02:58.768][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-13 16:02:58.770][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:02:58.771][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:02:58.772][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.773][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-13 16:02:58.775][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-12-13 16:02:58.777][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.778][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-12-13 16:02:58.779][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.780][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:02:58.782][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.783][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.784][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.785][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.787][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-13 16:02:58.788][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:02:58.789][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.790][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-12-13 16:02:58.791][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:02:58.793][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-12-13 16:02:58.793][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-13 16:02:58.794][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:58.795][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:58.796][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-13 16:02:58.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:58.799][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:58.800][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:02:58.801][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:58.802][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:58.803][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:02:58.805][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:02:58.805][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-13 16:02:58.805][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-13 16:02:58.806][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:02:58.807][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:02:58.808][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:58.809][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-13 16:02:58.817][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-12-13 16:02:58.819][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-13 16:02:58.821][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-13 16:02:58.823][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-12-13 16:02:58.824][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-13 16:02:58.826][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-12-13 16:02:58.846][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-12-13 16:02:58.862][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2025-12-13 16:02:58.872][biodb::testThat]
biodb.INFO [2025-12-13 16:02:58.873][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-13 16:02:58.874][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:02:58.875][biodb::testThat]
biodb.TRACE[2025-12-13 16:02:58.880][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2025-12-13 16:02:58.882][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-12-13 16:02:58.886][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-12-13 16:02:58.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-13 16:02:58.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:58.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:58.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:58.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:58.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:58.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-13 16:02:58.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:58.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:58.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:58.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:58.958][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-12-13 16:02:58.974][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:58.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:58.977][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.022][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-12-13 16:02:59.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.027][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.032][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.042][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-13 16:02:59.120][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2025-12-13 16:02:59.123][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.128][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.204][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:02:59.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:02:59.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.209][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:02:59.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:02:59.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.214][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-13 16:02:59.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-13 16:02:59.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.219][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-13 16:02:59.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-13 16:02:59.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.248][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.290][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.294][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.299][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.331][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.332][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.335][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.352][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-12-13 16:02:59.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.357][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.362][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.367][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-12-13 16:02:59.368][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.371][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.372][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-12-13 16:02:59.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.388][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.389][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.392][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.398][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.400][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.402][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.425][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2025-12-13 16:02:59.474][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-12-13 16:02:59.475][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-12-13 16:02:59.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-13 16:02:59.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:59.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:59.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:59.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:59.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:59.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-13 16:02:59.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.539][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-12-13 16:02:59.540][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.543][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.544][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-12-13 16:02:59.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.550][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.555][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.565][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-13 16:02:59.602][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2025-12-13 16:02:59.629][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.634][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.639][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:02:59.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:02:59.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.648][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:02:59.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:02:59.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.654][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-13 16:02:59.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-13 16:02:59.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.659][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-13 16:02:59.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-13 16:02:59.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.675][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.717][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.723][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.728][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:02:59.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.769][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.770][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.773][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.789][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-12-13 16:02:59.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.795][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.800][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.805][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-12-13 16:02:59.806][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.809][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.814][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-12-13 16:02:59.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.830][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.832][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:02:59.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.834][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:59.841][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:59.842][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:59.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:59.845][ef$get] fields variable is a list.
biodb.INFO [2025-12-13 16:02:59.855][biodb::testThat]
biodb.INFO [2025-12-13 16:02:59.856][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-13 16:02:59.858][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:02:59.859][biodb::testThat]
biodb.DEBUG[2025-12-13 16:02:59.862][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2025-12-13 16:02:59.865][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2025-12-13 16:02:59.868][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-12-13 16:02:59.870][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:02:59.871][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-13 16:02:59.873][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:02:59.874][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2025-12-13 16:03:00.059][biodb::testThat]
biodb.INFO [2025-12-13 16:03:00.060][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-13 16:03:00.061][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:00.062][biodb::testThat]
biodb.INFO [2025-12-13 16:03:00.070][biodb::testThat]
biodb.INFO [2025-12-13 16:03:00.072][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-13 16:03:00.073][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:00.074][biodb::testThat]
biodb.WARN [2025-12-13 16:03:00.098][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-12-13 16:03:00.129][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-12-13 16:03:00.140][biodb::testThat]
biodb.INFO [2025-12-13 16:03:00.142][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-13 16:03:00.143][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:00.144][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:00.168][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2025-12-13 16:03:00.233][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-12-13 16:03:00.278][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-12-13 16:03:00.279][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:03:00.281][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-13 16:03:00.282][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:03:00.283][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2025-12-13 16:03:00.378][biodb::testThat]
biodb.INFO [2025-12-13 16:03:00.379][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-13 16:03:00.380][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:00.382][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2025-12-13 16:03:00.439][biodb::testThat]
biodb.INFO [2025-12-13 16:03:00.441][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-13 16:03:00.442][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:00.443][biodb::testThat]
biodb.INFO [2025-12-13 16:03:00.453][biodb::testThat]
biodb.INFO [2025-12-13 16:03:00.454][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-13 16:03:00.456][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:00.457][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2025-12-13 16:03:00.519][biodb::testThat]
biodb.INFO [2025-12-13 16:03:00.521][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-13 16:03:00.522][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:00.523][biodb::testThat]
biodb.INFO [2025-12-13 16:03:00.531][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-13 16:03:00.533][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-12-13 16:03:00.534][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-13 16:03:00.535][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:00.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:00.538][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:00.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:00.540][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-12-13 16:03:00.554][biodb::testContext]
biodb.INFO [2025-12-13 16:03:00.555][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-13 16:03:00.557][biodb::testContext] Test context - Gene long tests
biodb.INFO [2025-12-13 16:03:00.558][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-13 16:03:00.559][biodb::testContext]
biodb.INFO [2025-12-13 16:03:00.561][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-13 16:03:00.563][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-12-13 16:03:00.567][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:00.569][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-13 16:03:00.570][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-13 16:03:00.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.575][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-13 16:03:00.576][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-13 16:03:00.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.581][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-13 16:03:00.582][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-13 16:03:00.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.587][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-13 16:03:00.588][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-13 16:03:00.590][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-13 16:03:00.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.594][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-13 16:03:00.596][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-13 16:03:00.597][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-13 16:03:00.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.602][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-13 16:03:00.603][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-13 16:03:00.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.608][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-13 16:03:00.609][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-13 16:03:00.610][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-13 16:03:00.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.615][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-13 16:03:00.616][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-13 16:03:00.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.621][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-13 16:03:00.622][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-13 16:03:00.623][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-13 16:03:00.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.628][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-13 16:03:00.629][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-13 16:03:00.630][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-13 16:03:00.632][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-13 16:03:00.633][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-13 16:03:00.634][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-13 16:03:00.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.639][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-13 16:03:00.640][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-13 16:03:00.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.645][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-13 16:03:00.646][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-13 16:03:00.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.656][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-13 16:03:00.657][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-13 16:03:00.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.661][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-13 16:03:00.663][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-13 16:03:00.664][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-13 16:03:00.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.669][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-13 16:03:00.670][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-13 16:03:00.681][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-13 16:03:00.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.684][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[2025-12-13 16:03:00.686][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-13 16:03:00.687][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-13 16:03:00.688][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-13 16:03:00.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.693][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-13 16:03:00.696][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:00.697][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-13 16:03:00.698][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:00.700][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:00.701][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:00.702][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:00.703][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:00.705][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:00.706][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-13 16:03:00.707][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:00.709][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:00.710][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-13 16:03:00.711][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:00.713][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:00.714][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:00.715][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:00.715][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:03:00.715][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:03:00.715][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-13 16:03:00.715][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-13 16:03:00.717][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:00.718][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:00.719][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:00.721][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:00.722][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:00.723][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:00.724][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:00.725][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:00.727][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:00.728][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:00.729][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:00.730][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:00.732][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-13 16:03:00.734][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:00.735][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-13 16:03:00.737][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:00.738][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:00.739][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:00.740][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:00.742][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:00.743][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:00.744][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-13 16:03:00.746][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:00.747][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:00.748][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-13 16:03:00.749][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:00.751][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:00.752][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:00.754][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:00.754][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:03:00.754][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:03:00.754][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-13 16:03:00.754][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-13 16:03:00.755][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:00.756][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:00.758][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:00.759][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:00.760][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:00.761][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:00.762][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:00.764][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:00.765][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:00.766][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:00.768][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:00.769][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:00.771][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-13 16:03:00.774][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:00.776][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-13 16:03:00.777][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:00.779][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:00.780][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:00.782][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:00.783][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:00.785][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:00.786][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-13 16:03:00.787][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:00.789][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:00.790][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-13 16:03:00.791][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:00.793][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:00.794][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:00.796][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:00.797][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:00.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:00.799][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:00.801][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:00.802][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:00.803][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:00.804][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:00.805][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:00.807][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:00.808][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:00.809][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:00.815][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:00.817][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-13 16:03:00.819][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:00.820][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-13 16:03:00.821][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:00.823][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:00.824][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:00.825][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:00.826][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:00.828][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:00.829][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-13 16:03:00.830][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:00.832][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:00.833][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-13 16:03:00.834][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:00.835][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:00.837][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:00.838][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:00.839][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:00.840][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:00.842][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:00.843][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:00.844][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:00.845][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:00.846][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:00.848][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:00.849][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:00.850][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:00.851][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:00.852][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:00.854][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:00.855][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:00.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:00.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:00.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:00.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:00.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:00.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.873][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[2025-12-13 16:03:00.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 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[2025-12-13 16:03:00.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:00.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:00.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:00.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:00.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:00.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:00.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:00.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:00.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:00.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:00.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:00.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:00.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:00.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:00.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:00.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:00.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:00.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:00.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:00.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:00.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:00.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:00.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:00.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:00.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:00.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:00.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:00.948][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-13 16:03:00.950][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-13 16:03:00.956][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-13 16:03:00.958][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-13 16:03:00.959][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-13 16:03:00.961][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-13 16:03:00.963][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-13 16:03:00.964][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-13 16:03:00.966][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-13 16:03:00.968][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-13 16:03:00.970][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-13 16:03:00.972][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-13 16:03:00.973][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-13 16:03:00.975][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-13 16:03:00.977][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-13 16:03:00.979][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-13 16:03:00.980][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-13 16:03:00.982][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-13 16:03:00.984][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-13 16:03:00.986][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-13 16:03:00.988][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-13 16:03:00.990][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-13 16:03:00.992][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-13 16:03:00.994][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-13 16:03:00.996][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-13 16:03:00.998][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-13 16:03:00.999][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-13 16:03:01.001][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-13 16:03:01.003][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-13 16:03:01.005][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-13 16:03:01.007][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-13 16:03:01.009][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-13 16:03:01.010][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-13 16:03:01.012][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-13 16:03:01.014][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-13 16:03:01.016][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-13 16:03:01.017][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-13 16:03:01.019][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-13 16:03:01.021][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-13 16:03:01.022][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-13 16:03:01.024][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-13 16:03:01.026][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-13 16:03:01.028][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-13 16:03:01.029][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-13 16:03:01.031][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-13 16:03:01.033][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-13 16:03:01.034][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-13 16:03:01.036][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-13 16:03:01.038][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-13 16:03:01.040][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-13 16:03:01.041][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-13 16:03:01.043][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-13 16:03:01.045][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-13 16:03:01.046][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-13 16:03:01.048][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-13 16:03:01.050][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-13 16:03:01.051][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-13 16:03:01.053][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-13 16:03:01.055][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-13 16:03:01.056][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-13 16:03:01.058][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-13 16:03:01.060][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-13 16:03:01.061][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-13 16:03:01.063][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-13 16:03:01.065][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-13 16:03:01.066][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-13 16:03:01.068][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-13 16:03:01.070][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-13 16:03:01.071][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-13 16:03:01.073][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-13 16:03:01.075][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-13 16:03:01.077][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-13 16:03:01.078][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-13 16:03:01.080][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-13 16:03:01.082][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-13 16:03:01.084][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-13 16:03:01.085][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-13 16:03:01.087][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-13 16:03:01.089][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-13 16:03:01.095][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-13 16:03:01.097][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-13 16:03:01.098][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-13 16:03:01.100][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-13 16:03:01.101][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-13 16:03:01.103][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-13 16:03:01.105][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:01.106][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:01.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:01.108][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:01.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:01.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:01.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:01.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:01.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:01.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:01.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:01.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:01.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:01.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:01.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:01.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:01.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:01.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:01.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:01.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:01.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:01.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:01.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:01.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:01.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:01.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:01.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:01.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:01.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:01.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:01.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:01.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:01.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:01.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:01.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:01.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:01.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:01.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:01.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:01.148][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[2025-12-13 16:03:01.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:01.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:01.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:01.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:01.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:01.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:01.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:01.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:01.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:01.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:01.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:01.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:01.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:01.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:01.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:01.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:01.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:01.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:01.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:01.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:01.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:01.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:01.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:01.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:01.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:01.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:01.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:01.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:01.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:01.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:01.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:01.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:01.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:01.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:01.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:01.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:01.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:01.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:01.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:01.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:01.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:01.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:01.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:01.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:01.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:01.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:01.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:01.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:01.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:01.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:01.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:01.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:01.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:01.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:01.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:01.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:01.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:01.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:01.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:01.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:01.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:01.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:01.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:01.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:01.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:01.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:01.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:01.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:01.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:01.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:01.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:01.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:01.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:01.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:01.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:01.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:01.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:01.241][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-12-13 16:03:01.243][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-12-13 16:03:01.245][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.246][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-12-13 16:03:01.248][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.249][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:01.250][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.251][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:01.253][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.254][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:01.255][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-12-13 16:03:01.256][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:01.258][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.259][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-12-13 16:03:01.260][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:01.262][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-12-13 16:03:01.262][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-12-13 16:03:01.263][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:01.264][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:01.265][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-13 16:03:01.267][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:01.268][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:01.269][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:01.270][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:01.271][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:01.272][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:01.274][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-13 16:03:01.274][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-12-13 16:03:01.275][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:01.276][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:01.277][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.278][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:01.280][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-12-13 16:03:01.282][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.284][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-12-13 16:03:01.285][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.286][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:01.287][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.289][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:01.290][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.291][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:01.292][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-13 16:03:01.294][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:01.295][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.296][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-12-13 16:03:01.298][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:01.299][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-12-13 16:03:01.299][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-12-13 16:03:01.299][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-12-13 16:03:01.299][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-12-13 16:03:01.299][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-12-13 16:03:01.299][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-12-13 16:03:01.300][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:01.302][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:01.303][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-13 16:03:01.304][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:01.305][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:01.306][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:01.308][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:01.309][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:01.310][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:01.311][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:01.311][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-13 16:03:01.312][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:01.314][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:01.315][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.316][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:01.318][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-12-13 16:03:01.320][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:01.321][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-12-13 16:03:01.323][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.324][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:01.325][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.326][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:01.328][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.329][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:01.330][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-13 16:03:01.331][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:01.333][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.334][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-12-13 16:03:01.335][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:01.336][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-13 16:03:01.336][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:01.336][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:01.336][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:01.336][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:01.336][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:01.336][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:01.336][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:01.336][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:01.336][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:01.336][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-12-13 16:03:01.336][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:01.336][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:01.336][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:01.338][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:01.339][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:01.339][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:03:01.339][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:03:01.341][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-13 16:03:01.342][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:01.343][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:01.344][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:01.345][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:01.346][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:01.348][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:01.349][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:01.349][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-13 16:03:01.349][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-13 16:03:01.350][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:01.351][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:01.352][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.354][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-13 16:03:01.355][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-12-13 16:03:01.358][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.359][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-12-13 16:03:01.360][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.361][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:01.363][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.364][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:01.365][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.366][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:01.372][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-13 16:03:01.373][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:01.374][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.375][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-12-13 16:03:01.377][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:01.378][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-12-13 16:03:01.378][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-13 16:03:01.379][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:01.380][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:01.382][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-13 16:03:01.383][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:01.384][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:01.385][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:01.386][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:01.388][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:01.389][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:01.390][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:01.390][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-13 16:03:01.390][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-13 16:03:01.391][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:01.393][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:01.394][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:01.395][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-13 16:03:01.397][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-12-13 16:03:01.399][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-13 16:03:01.400][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-13 16:03:01.402][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-12-13 16:03:01.404][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-13 16:03:01.406][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-12-13 16:03:01.415][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2025-12-13 16:03:01.457][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2025-12-13 16:03:01.462][biodb::testThat]
biodb.INFO [2025-12-13 16:03:01.465][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-13 16:03:01.466][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:01.468][biodb::testThat]
biodb.TRACE[2025-12-13 16:03:01.474][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2025-12-13 16:03:01.476][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-12-13 16:03:01.480][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-12-13 16:03:01.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-13 16:03:01.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:01.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:01.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:01.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:01.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:01.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-13 16:03:01.509][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:01.511][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:01.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.513][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:01.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:01.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.520][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-13 16:03:01.521][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-13 16:03:01.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.529][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.531][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-13 16:03:01.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-13 16:03:01.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.536][ef$get] Asked field names are: location.
biodb.TRACE[2025-12-13 16:03:01.538][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-12-13 16:03:01.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.540][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.543][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-12-13 16:03:01.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-12-13 16:03:01.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.548][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-12-13 16:03:01.549][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-12-13 16:03:01.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.552][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.554][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-12-13 16:03:01.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-12-13 16:03:01.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.559][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-12-13 16:03:01.560][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:01.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.563][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.565][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-12-13 16:03:01.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:01.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.570][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-12-13 16:03:01.572][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-12-13 16:03:01.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.574][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.577][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-12-13 16:03:01.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-12-13 16:03:01.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.587][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:03:01.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:03:01.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.593][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-12-13 16:03:01.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-12-13 16:03:01.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.598][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-12-13 16:03:01.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-12-13 16:03:01.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:01.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:01.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.608][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-12-13 16:03:01.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-12-13 16:03:01.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:01.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:01.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:01.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:01.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:01.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:01.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:01.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:01.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:01.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:01.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:01.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:01.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-13 16:03:01.644][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2025-12-13 16:03:01.647][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-13 16:03:01.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:03:01.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.653][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-13 16:03:01.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:03:01.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.661][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:03:01.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:03:01.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.667][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:03:01.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:03:01.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:01.677][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:03:01.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:03:01.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-13 16:03:01.682][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-12-13 16:03:01.723][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-12-13 16:03:01.743][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2025-12-13 16:03:01.745][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2025-12-13 16:03:01.747][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-12-13 16:03:01.749][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-12-13 16:03:01.751][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:03:01.752][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-13 16:03:01.753][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:03:01.754][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-13 16:03:01.819][biodb::testThat]
biodb.INFO [2025-12-13 16:03:01.820][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-13 16:03:01.821][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:01.822][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:01.825][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2025-12-13 16:03:01.827][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2025-12-13 16:03:01.829][cch$loadContents] Load 8 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-12-13 16:03:01.830][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:03:01.832][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:01.833][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:03:01.834][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-13 16:03:01.835][private$retrieveContents] Get entry content(s) for 8 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-13 16:03:01.901][biodb::testThat]
biodb.INFO [2025-12-13 16:03:01.902][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-13 16:03:01.903][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:01.904][biodb::testThat]
biodb.TRACE[2025-12-13 16:03:01.908][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:01.910][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:01.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:01.912][ef$get] fields variable is a list.
biodb.DEBUG[2025-12-13 16:03:01.914][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2025-12-13 16:03:01.930][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-12-13 16:03:01.931][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-12-13 16:03:01.933][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-12-13 16:03:01.935][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:03:01.936][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:01.937][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:03:01.938][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-13 16:03:01.963][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-13 16:03:02.052][biodb::testThat]
biodb.INFO [2025-12-13 16:03:02.054][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-13 16:03:02.055][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:02.056][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:02.066][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-12-13 16:03:02.068][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-12-13 16:03:02.070][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-12-13 16:03:02.071][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:03:02.073][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:02.074][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:03:02.075][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-13 16:03:02.076][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-13 16:03:02.138][biodb::testThat]
biodb.INFO [2025-12-13 16:03:02.139][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-13 16:03:02.141][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:02.142][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:02.147][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-12-13 16:03:02.149][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-12-13 16:03:02.150][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-12-13 16:03:02.152][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:03:02.153][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:02.155][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:03:02.156][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-13 16:03:02.157][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-13 16:03:02.249][biodb::testThat]
biodb.INFO [2025-12-13 16:03:02.251][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-13 16:03:02.252][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:02.253][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-13 16:03:02.381][biodb::testThat]
biodb.INFO [2025-12-13 16:03:02.382][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-13 16:03:02.383][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:02.385][biodb::testThat]
biodb.INFO [2025-12-13 16:03:02.396][biodb::testThat]
biodb.INFO [2025-12-13 16:03:02.397][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-13 16:03:02.398][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:02.399][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-13 16:03:02.458][biodb::testThat]
biodb.INFO [2025-12-13 16:03:02.460][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-13 16:03:02.461][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:02.462][biodb::testThat]
biodb.INFO [2025-12-13 16:03:02.470][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-13 16:03:02.472][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2025-12-13 16:03:02.473][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-12-13 16:03:02.474][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-13 16:03:02.476][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:02.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:02.478][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:02.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:02.480][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-12-13 16:03:02.486][biodb::testContext]
biodb.INFO [2025-12-13 16:03:02.488][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-13 16:03:02.489][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2025-12-13 16:03:02.490][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-13 16:03:02.491][biodb::testContext]
biodb.INFO [2025-12-13 16:03:02.494][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-13 16:03:02.496][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-12-13 16:03:02.500][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:02.502][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-13 16:03:02.503][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-13 16:03:02.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.513][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-13 16:03:02.514][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-13 16:03:02.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.519][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-13 16:03:02.521][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-13 16:03:02.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.525][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-13 16:03:02.526][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-13 16:03:02.528][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-13 16:03:02.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.532][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-13 16:03:02.533][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-13 16:03:02.535][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-13 16:03:02.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.539][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-13 16:03:02.541][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-13 16:03:02.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.545][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-13 16:03:02.546][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-13 16:03:02.548][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-13 16:03:02.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.552][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-13 16:03:02.553][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-13 16:03:02.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.558][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-13 16:03:02.559][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-13 16:03:02.561][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-13 16:03:02.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.565][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-13 16:03:02.566][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-13 16:03:02.568][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-13 16:03:02.569][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-13 16:03:02.570][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-13 16:03:02.572][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-13 16:03:02.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.576][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-13 16:03:02.577][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-13 16:03:02.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.582][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-13 16:03:02.583][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-13 16:03:02.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.588][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-13 16:03:02.589][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-13 16:03:02.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.594][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-13 16:03:02.595][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-13 16:03:02.597][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-13 16:03:02.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.601][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-13 16:03:02.603][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-13 16:03:02.613][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-13 16:03:02.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.618][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-13 16:03:02.619][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-13 16:03:02.621][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-13 16:03:02.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.625][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-13 16:03:02.628][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:02.629][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-13 16:03:02.630][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:02.631][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:02.633][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:02.634][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:02.635][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:02.636][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:02.638][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-13 16:03:02.639][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:02.640][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:02.641][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-13 16:03:02.643][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:02.644][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:02.645][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:02.646][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:02.646][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:03:02.646][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:03:02.646][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-13 16:03:02.646][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-13 16:03:02.648][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:02.653][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:02.655][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:02.656][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:02.658][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:02.659][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:02.660][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:02.661][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:02.662][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:02.664][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:02.665][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:02.666][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:02.668][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-13 16:03:02.670][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:02.671][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-13 16:03:02.673][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:02.674][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:02.676][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:02.677][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:02.678][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:02.680][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:02.681][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-13 16:03:02.682][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:02.683][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:02.685][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-13 16:03:02.686][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:02.687][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:02.688][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:02.690][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:02.690][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:03:02.690][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:03:02.690][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-13 16:03:02.690][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-13 16:03:02.691][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:02.692][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:02.693][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:02.695][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:02.696][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:02.697][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:02.698][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:02.699][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:02.701][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:02.702][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:02.703][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:02.704][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:02.706][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-13 16:03:02.708][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:02.709][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-13 16:03:02.711][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:02.712][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:02.713][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:02.714][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:02.716][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:02.717][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:02.718][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-13 16:03:02.720][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:02.721][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:02.722][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-13 16:03:02.723][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:02.725][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:02.726][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:02.727][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:02.729][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:02.730][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:02.731][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:02.732][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:02.734][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:02.735][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:02.736][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:02.737][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:02.738][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:02.740][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:02.741][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:02.742][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:02.744][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-13 16:03:02.746][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:02.747][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-13 16:03:02.748][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:02.749][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:02.751][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:02.752][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:02.753][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:02.754][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:02.756][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-13 16:03:02.757][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:02.758][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:02.760][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-13 16:03:02.761][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:02.762][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:02.763][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:02.765][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:02.766][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:02.767][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:02.768][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:02.769][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:02.771][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:02.772][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:02.773][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:02.774][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:02.776][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:02.777][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:02.778][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:02.779][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:02.781][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:02.782][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.788][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[2025-12-13 16:03:02.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:02.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:02.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:02.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:02.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:02.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:02.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:02.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:02.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:02.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:02.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:02.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:02.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:02.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:02.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:02.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:02.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.833][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[2025-12-13 16:03:02.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:02.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:02.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:02.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:02.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:02.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:02.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:02.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:02.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:02.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:02.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:02.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:02.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.866][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[2025-12-13 16:03:02.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:02.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:02.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:02.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:02.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:02.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:02.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:02.881][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-13 16:03:02.886][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-13 16:03:02.890][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-13 16:03:02.895][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-13 16:03:02.899][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-13 16:03:02.904][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-13 16:03:02.907][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-13 16:03:02.912][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-13 16:03:02.916][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-13 16:03:02.920][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-13 16:03:02.923][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-13 16:03:02.927][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-13 16:03:02.930][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-13 16:03:02.934][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-13 16:03:02.937][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-13 16:03:02.940][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-13 16:03:02.944][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-13 16:03:02.947][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-13 16:03:02.951][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-13 16:03:02.954][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-13 16:03:02.965][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-13 16:03:02.968][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-13 16:03:02.971][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-13 16:03:02.974][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-13 16:03:02.977][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-13 16:03:02.981][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-13 16:03:02.984][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-13 16:03:02.988][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-13 16:03:02.991][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-13 16:03:02.995][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-13 16:03:02.998][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-13 16:03:03.001][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-13 16:03:03.004][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-13 16:03:03.007][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-13 16:03:03.010][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-13 16:03:03.013][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-13 16:03:03.016][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-13 16:03:03.018][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-13 16:03:03.020][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-13 16:03:03.023][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-13 16:03:03.024][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-13 16:03:03.026][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-13 16:03:03.028][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-13 16:03:03.031][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-13 16:03:03.034][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-13 16:03:03.036][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-13 16:03:03.038][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-13 16:03:03.040][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-13 16:03:03.043][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-13 16:03:03.047][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-13 16:03:03.049][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-13 16:03:03.051][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-13 16:03:03.053][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-13 16:03:03.055][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-13 16:03:03.056][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-13 16:03:03.058][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-13 16:03:03.060][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-13 16:03:03.063][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-13 16:03:03.066][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-13 16:03:03.067][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-13 16:03:03.069][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-13 16:03:03.071][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-13 16:03:03.072][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-13 16:03:03.074][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-13 16:03:03.076][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-13 16:03:03.077][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-13 16:03:03.079][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-13 16:03:03.081][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-13 16:03:03.082][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-13 16:03:03.084][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-13 16:03:03.086][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-13 16:03:03.088][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-13 16:03:03.089][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-13 16:03:03.091][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-13 16:03:03.093][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-13 16:03:03.094][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-13 16:03:03.096][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-13 16:03:03.098][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-13 16:03:03.099][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-13 16:03:03.101][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-13 16:03:03.103][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-13 16:03:03.104][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-13 16:03:03.106][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-13 16:03:03.108][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-13 16:03:03.109][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-13 16:03:03.111][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:03.112][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:03.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:03.114][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:03.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:03.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:03.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:03.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:03.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:03.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:03.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:03.128][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[2025-12-13 16:03:03.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:03.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:03.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:03.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:03.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:03.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:03.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:03.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:03.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:03.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:03.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:03.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:03.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:03.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:03.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:03.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:03.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:03.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:03.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:03.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:03.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:03.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:03.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:03.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:03.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:03.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:03.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:03.158][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[2025-12-13 16:03:03.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:03.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:03.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:03.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:03.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:03.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:03.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:03.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:03.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:03.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:03.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:03.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:03.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:03.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:03.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:03.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:03.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:03.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:03.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:03.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:03.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:03.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:03.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:03.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:03.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:03.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:03.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:03.189][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[2025-12-13 16:03:03.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:03.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:03.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:03.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:03.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:03.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:03.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:03.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:03.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:03.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:03.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:03.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:03.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:03.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:03.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:03.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:03.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:03.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:03.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:03.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:03.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:03.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:03.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:03.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:03.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:03.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:03.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:03.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:03.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:03.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:03.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:03.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:03.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:03.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:03.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:03.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:03.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:03.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:03.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:03.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:03.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:03.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:03.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:03.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:03.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:03.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:03.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:03.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:03.242][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[2025-12-13 16:03:03.250][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-12-13 16:03:03.253][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-12-13 16:03:03.256][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.257][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-12-13 16:03:03.258][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.260][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:03.261][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.262][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:03.264][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.265][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:03.266][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-12-13 16:03:03.267][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:03.269][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.270][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-12-13 16:03:03.272][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:03.273][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-12-13 16:03:03.273][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-12-13 16:03:03.275][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:03.276][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:03.277][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-13 16:03:03.278][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:03.279][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:03.281][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:03.282][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:03.283][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:03.284][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:03.286][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-13 16:03:03.286][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-12-13 16:03:03.287][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:03.288][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:03.289][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.291][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:03.292][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-12-13 16:03:03.294][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.296][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-12-13 16:03:03.297][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.298][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:03.299][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.301][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:03.302][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.303][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:03.304][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-13 16:03:03.306][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:03.307][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.308][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-12-13 16:03:03.309][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:03.311][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-12-13 16:03:03.311][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-12-13 16:03:03.311][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-12-13 16:03:03.311][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-12-13 16:03:03.311][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-12-13 16:03:03.311][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-12-13 16:03:03.312][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:03.313][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:03.315][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-13 16:03:03.316][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:03.317][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:03.318][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:03.319][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:03.320][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:03.322][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:03.323][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:03.323][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-13 16:03:03.324][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:03.325][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:03.327][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.328][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:03.329][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-12-13 16:03:03.332][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:03.333][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-12-13 16:03:03.334][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.335][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:03.337][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.338][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:03.339][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.340][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:03.342][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-13 16:03:03.343][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:03.344][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.346][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-12-13 16:03:03.347][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:03.348][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-13 16:03:03.348][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:03.348][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:03.348][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:03.348][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:03.348][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:03.348][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:03.348][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:03.348][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:03.348][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:03.348][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-12-13 16:03:03.348][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:03.348][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:03.348][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:03.350][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:03.351][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:03.351][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:03:03.351][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:03:03.352][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-13 16:03:03.354][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:03.355][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:03.356][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:03.357][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:03.358][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:03.360][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:03.361][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:03.361][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-13 16:03:03.361][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-13 16:03:03.362][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:03.363][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:03.365][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.366][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-13 16:03:03.368][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-12-13 16:03:03.370][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.371][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-12-13 16:03:03.372][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.374][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:03.375][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.376][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:03.377][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.383][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:03.384][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-13 16:03:03.385][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:03.387][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.388][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-12-13 16:03:03.389][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:03.390][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-12-13 16:03:03.390][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-13 16:03:03.392][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:03.393][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:03.394][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-13 16:03:03.395][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:03.396][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:03.398][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:03.399][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:03.400][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:03.401][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:03.403][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:03.403][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-13 16:03:03.403][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-13 16:03:03.404][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:03.405][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:03.406][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:03.407][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-13 16:03:03.409][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-12-13 16:03:03.411][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-13 16:03:03.413][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-13 16:03:03.414][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-12-13 16:03:03.416][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-13 16:03:03.418][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-12-13 16:03:03.427][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2025-12-13 16:03:03.435][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2025-12-13 16:03:03.440][biodb::testThat]
biodb.INFO [2025-12-13 16:03:03.441][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-13 16:03:03.442][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:03.443][biodb::testThat]
biodb.TRACE[2025-12-13 16:03:03.447][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2025-12-13 16:03:03.448][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-12-13 16:03:03.452][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-12-13 16:03:03.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-13 16:03:03.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:03.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:03.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:03.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:03.465][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:03.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-13 16:03:03.471][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:03.473][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:03.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.475][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:03.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:03.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.482][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:03.483][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:03.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.486][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.488][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:03.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:03.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.493][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:03.494][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:03.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.497][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:03.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:03.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.503][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:03.505][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:03.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.507][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.509][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:03.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:03.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.520][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:03.521][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:03.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.524][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.525][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:03.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:03.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.530][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:03.532][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:03.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.534][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.536][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:03.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:03.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.541][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-13 16:03:03.542][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:03.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.544][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.546][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-13 16:03:03.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:03.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.551][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:03.552][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:03.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.555][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.556][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:03.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:03.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.561][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:03.563][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:03.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.565][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.567][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:03.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:03.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.572][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:03.573][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:03.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.576][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:03.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:03.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.582][ef$get] Asked field names are: logp.
biodb.TRACE[2025-12-13 16:03:03.584][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-13 16:03:03.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.586][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.588][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-13 16:03:03.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-13 16:03:03.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.593][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-13 16:03:03.594][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:03.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.596][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-13 16:03:03.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:03.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.603][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:03.605][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:03.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.607][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.609][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:03.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:03.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.614][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:03.615][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:03.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.617][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.619][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:03.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:03.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.624][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-12-13 16:03:03.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:03.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.629][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:03.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:03.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.634][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:03.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:03.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.643][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-12-13 16:03:03.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:03.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.648][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:03.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:03.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.653][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:03.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:03.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.658][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-12-13 16:03:03.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:03.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.663][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:03.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:03.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.668][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:03.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:03.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.675][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-12-13 16:03:03.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:03.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.683][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:03.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:03.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.691][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:03.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:03.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.701][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-12-13 16:03:03.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:03.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.711][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:03.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:03.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.722][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:03.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:03.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.754][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:03.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:03.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.769][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:03.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:03.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.780][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:03.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:03.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:03.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:03.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.800][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:03.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:03.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:03.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:03.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:03.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:03.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:03.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:03.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:03.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:03.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:03.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:03.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:03.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:03.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-13 16:03:03.871][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2025-12-13 16:03:03.876][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-13 16:03:03.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:03:03.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.885][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-13 16:03:03.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:03:03.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.894][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:03:03.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:03:03.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.903][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:03:03.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:03:03.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.913][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:03:03.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:03:03.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.922][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-13 16:03:03.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-13 16:03:03.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.931][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-13 16:03:03.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-13 16:03:03.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:03.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:03.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.961][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:03.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:03.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:03.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:03.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:03.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:03.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:03.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:03.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:04.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:04.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:04.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:04.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:04.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:04.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:04.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:04.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.042][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:04.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:04.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.052][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:04.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:04.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.061][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:04.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:04.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:04.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:04.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:04.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:04.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:04.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:04.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.106][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:04.107][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:04.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.110][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:04.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:04.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.127][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-13 16:03:04.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:04.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:04.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:04.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:04.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:04.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.142][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-13 16:03:04.144][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:04.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.146][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.147][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-13 16:03:04.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:04.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-13 16:03:04.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:04.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:04.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:04.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:04.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:04.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.178][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-13 16:03:04.180][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:04.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.182][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-13 16:03:04.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:04.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.199][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:04.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:04.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.204][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:04.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:04.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.209][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:04.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:04.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.214][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:04.220][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:04.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.223][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.224][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:04.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:04.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.239][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-13 16:03:04.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-13 16:03:04.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.245][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-13 16:03:04.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-13 16:03:04.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.250][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-13 16:03:04.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-13 16:03:04.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.255][ef$get] Asked field names are: logp.
biodb.TRACE[2025-12-13 16:03:04.256][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-13 16:03:04.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.259][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.260][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-13 16:03:04.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-13 16:03:04.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.276][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:04.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:04.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.281][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:04.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:04.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.286][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:04.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:04.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.291][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:04.292][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:04.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.295][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.296][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:04.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:04.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.311][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:04.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:04.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.316][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:04.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:04.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.321][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:04.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:04.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.326][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:04.328][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:04.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.330][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.331][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:04.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:04.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.352][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:04.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:04.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.357][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:04.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:04.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.362][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:04.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:04.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.367][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:04.368][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:04.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.371][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.372][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:04.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:04.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.387][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:04.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:04.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.392][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:04.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:04.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.397][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:04.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:04.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.402][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:04.404][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:04.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.406][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.407][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:04.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:04.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.422][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:04.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:04.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.427][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:04.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:04.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.432][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:04.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:04.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.438][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:04.439][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:04.440][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.441][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.443][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:04.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:04.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.458][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:04.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:04.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.463][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:04.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:04.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.473][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:04.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:04.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.478][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:04.479][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:04.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.482][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.483][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:04.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:04.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:04.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:04.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.503][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:04.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:04.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.508][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:04.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:04.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.513][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:04.515][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:04.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.517][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.518][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:04.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:04.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.534][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:04.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:04.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.539][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:04.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:04.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:04.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:04.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.549][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:04.550][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:04.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.553][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.554][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:04.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:04.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:04.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:04.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:04.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:04.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:04.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:04.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.585][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:04.587][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:04.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.594][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:04.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:04.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.612][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:04.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:04.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.618][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:04.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:04.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.623][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:04.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:04.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.628][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:04.629][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:04.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.632][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.633][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:04.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:04.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.649][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:04.650][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:04.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.653][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.659][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:04.660][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:04.662][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.663][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.669][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:04.671][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:04.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.673][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.680][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:04.681][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:04.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.684][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.690][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:04.692][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:04.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.694][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.701][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:04.702][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:04.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.705][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.711][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:04.713][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:04.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.715][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.726][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:04.728][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:04.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.731][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.737][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:04.739][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:04.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.741][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.748][ef$get] Asked field names are: logp.
biodb.TRACE[2025-12-13 16:03:04.749][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-13 16:03:04.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.752][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.759][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:04.760][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:04.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.763][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.769][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:04.771][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:04.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.773][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.780][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:04.782][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:04.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.784][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.791][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:04.793][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:04.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.795][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.802][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:04.803][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:04.804][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.806][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.813][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2025-12-13 16:03:04.815][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-12-13 16:03:04.816][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-12-13 16:03:04.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-13 16:03:04.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:04.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:04.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:04.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:04.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:04.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-13 16:03:04.834][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:04.836][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:04.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.839][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:04.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:04.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.846][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:04.847][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:04.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.850][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.851][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:04.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:04.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.857][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:04.858][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:04.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.865][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.867][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:04.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:04.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.873][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:04.874][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:04.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.876][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.878][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:04.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:04.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.883][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:04.884][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:04.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.887][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.888][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:04.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:04.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.893][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:04.895][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:04.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.897][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.899][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:04.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:04.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.904][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-13 16:03:04.905][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:04.906][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.908][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.909][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-13 16:03:04.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:04.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.914][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:04.916][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:04.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.918][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.920][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:04.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:04.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.925][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:04.926][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:04.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.928][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.930][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:04.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:04.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.935][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:04.936][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:04.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.939][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.940][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:04.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:04.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.945][ef$get] Asked field names are: logp.
biodb.TRACE[2025-12-13 16:03:04.947][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-13 16:03:04.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.949][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.951][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-13 16:03:04.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-13 16:03:04.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.956][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-13 16:03:04.957][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:04.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.959][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-13 16:03:04.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:04.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.966][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:04.967][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:04.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.970][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.971][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:04.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:04.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.977][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:04.978][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:04.979][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.980][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.982][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:04.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:04.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.992][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-12-13 16:03:04.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:04.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:04.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:04.997][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:04.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:05.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.002][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:05.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:05.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.007][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-12-13 16:03:05.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:05.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.013][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:05.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:05.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.018][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:05.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:05.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.023][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-12-13 16:03:05.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:05.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.028][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:05.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:05.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.033][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:05.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:05.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.038][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-12-13 16:03:05.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:05.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.043][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:05.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:05.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.048][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:05.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:05.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.053][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-12-13 16:03:05.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:05.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.058][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:05.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:05.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.064][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:05.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:05.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.070][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:05.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:05.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.076][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:05.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:05.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.082][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:05.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:05.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.092][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:05.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:05.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-13 16:03:05.134][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2025-12-13 16:03:05.137][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-13 16:03:05.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:03:05.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.142][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-13 16:03:05.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:03:05.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.147][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:03:05.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:03:05.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.152][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:03:05.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:03:05.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.157][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:03:05.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:03:05.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.162][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-13 16:03:05.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-13 16:03:05.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.167][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-13 16:03:05.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-13 16:03:05.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.183][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:05.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:05.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.226][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:05.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:05.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.231][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:05.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:05.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.246][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:05.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:05.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.274][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.275][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.277][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:05.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:05.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:05.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:05.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:05.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:05.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.309][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:05.311][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:05.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.313][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:05.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:05.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:05.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:05.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:05.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:05.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:05.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:05.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.345][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:05.347][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:05.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.349][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.350][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:05.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:05.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.370][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:05.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:05.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.376][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:05.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:05.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.381][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:05.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:05.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.386][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:05.387][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:05.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.390][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.391][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:05.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:05.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.406][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-13 16:03:05.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-13 16:03:05.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.412][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-13 16:03:05.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-13 16:03:05.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.417][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-13 16:03:05.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-13 16:03:05.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.422][ef$get] Asked field names are: logp.
biodb.TRACE[2025-12-13 16:03:05.423][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-13 16:03:05.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.425][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.427][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-13 16:03:05.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-13 16:03:05.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.442][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:05.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:05.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.448][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:05.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:05.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.453][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:05.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:05.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.458][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:05.459][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:05.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.462][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.463][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:05.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:05.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.479][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:05.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:05.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.484][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:05.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:05.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.489][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:05.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:05.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.499][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:05.501][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:05.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.504][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.505][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:05.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:05.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.521][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:05.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:05.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.526][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:05.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:05.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.531][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:05.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:05.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.537][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:05.538][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:05.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.540][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.542][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:05.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:05.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.557][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:05.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:05.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.563][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:05.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:05.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:05.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:05.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.573][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:05.574][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:05.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.577][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.578][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:05.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:05.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.594][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:05.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:05.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.599][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:05.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:05.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.605][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:05.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:05.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.610][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:05.611][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:05.613][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.614][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.615][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:05.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:05.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.638][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:05.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:05.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.644][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:05.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:05.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.649][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:05.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:05.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.655][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:05.656][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:05.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.658][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.660][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:05.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:05.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.675][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:05.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:05.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.680][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:05.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:05.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.685][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:05.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:05.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.690][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:05.691][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:05.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.694][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.695][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:05.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:05.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.710][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:05.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:05.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.715][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:05.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:05.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.720][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:05.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:05.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.725][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:05.727][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:05.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.729][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.730][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:05.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:05.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.745][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:05.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:05.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.755][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:05.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:05.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.760][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:05.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:05.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.765][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:05.766][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:05.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.769][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.770][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:05.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:05.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.785][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:05.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:05.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:05.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:05.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:05.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:05.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.800][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:05.801][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:05.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.804][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.805][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:05.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:05.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.820][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:05.821][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:05.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.824][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.830][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:05.831][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-13 16:03:05.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.834][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.840][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:05.842][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-13 16:03:05.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.844][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.850][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:05.852][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-13 16:03:05.853][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.854][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.860][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:05.862][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:03:05.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.864][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.870][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:05.872][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:03:05.873][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.874][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.885][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:05.886][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:05.888][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.889][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.895][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:05.897][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:05.898][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.899][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.905][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:05.906][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:05.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.909][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.915][ef$get] Asked field names are: logp.
biodb.TRACE[2025-12-13 16:03:05.916][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-13 16:03:05.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.919][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.925][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:05.926][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:05.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.929][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.935][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:05.936][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:03:05.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.939][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.945][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:05.946][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:05.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.949][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.955][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:05.956][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-13 16:03:05.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.959][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:05.965][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:05.967][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-13 16:03:05.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:05.969][ef$get] fields variable is a list.
biodb.INFO [2025-12-13 16:03:05.979][biodb::testThat]
biodb.INFO [2025-12-13 16:03:05.980][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-13 16:03:05.981][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:05.983][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:05.985][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-12-13 16:03:05.988][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-12-13 16:03:05.990][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-13 16:03:05.991][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:03:05.993][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:05.994][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:03:05.995][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-13 16:03:05.996][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-13 16:03:06.059][biodb::testThat]
biodb.INFO [2025-12-13 16:03:06.060][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-13 16:03:06.062][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:06.063][biodb::testThat]
biodb.TRACE[2025-12-13 16:03:06.067][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:06.068][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:06.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:06.070][ef$get] fields variable is a list.
biodb.DEBUG[2025-12-13 16:03:06.072][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2025-12-13 16:03:06.083][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-12-13 16:03:06.085][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-12-13 16:03:06.087][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-13 16:03:06.088][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:03:06.089][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:06.091][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:03:06.092][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-13 16:03:06.093][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-13 16:03:06.155][biodb::testThat]
biodb.INFO [2025-12-13 16:03:06.156][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-13 16:03:06.158][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:06.159][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:06.168][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-12-13 16:03:06.170][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-12-13 16:03:06.172][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-13 16:03:06.173][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:03:06.174][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:06.176][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:03:06.177][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-13 16:03:06.178][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-13 16:03:06.242][biodb::testThat]
biodb.INFO [2025-12-13 16:03:06.243][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-13 16:03:06.244][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:06.245][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:06.250][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-12-13 16:03:06.252][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-12-13 16:03:06.253][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-13 16:03:06.255][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:03:06.256][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:06.257][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:03:06.259][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-13 16:03:06.260][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-13 16:03:06.319][biodb::testThat]
biodb.INFO [2025-12-13 16:03:06.320][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-13 16:03:06.321][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:06.322][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-13 16:03:06.387][biodb::testThat]
biodb.INFO [2025-12-13 16:03:06.388][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-13 16:03:06.389][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:06.390][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-13 16:03:06.448][biodb::testThat]
biodb.INFO [2025-12-13 16:03:06.449][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-13 16:03:06.454][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:06.456][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-13 16:03:06.514][biodb::testThat]
biodb.INFO [2025-12-13 16:03:06.515][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-13 16:03:06.516][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:06.518][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2025-12-13 16:03:06.590][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:06.592][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:06.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:06.594][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:06.595][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:06.597][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:06.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:06.599][ef$get] fields variable is a list.
biodb.INFO [2025-12-13 16:03:06.601][biodb::testThat]
biodb.INFO [2025-12-13 16:03:06.602][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-12-13 16:03:06.604][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:06.605][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:06.614][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-12-13 16:03:06.615][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-12-13 16:03:06.617][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-13 16:03:06.619][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:03:06.620][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:06.621][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:03:06.622][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-13 16:03:06.624][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-13 16:03:06.687][biodb::testThat]
biodb.INFO [2025-12-13 16:03:06.688][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-12-13 16:03:06.689][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:06.690][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:06.694][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-12-13 16:03:06.695][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-12-13 16:03:06.697][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-13 16:03:06.698][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:03:06.700][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:06.701][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:03:06.702][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-13 16:03:06.703][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-13 16:03:06.761][biodb::testThat]
biodb.INFO [2025-12-13 16:03:06.762][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-12-13 16:03:06.764][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:06.765][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:06.768][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-12-13 16:03:06.770][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-12-13 16:03:06.771][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-13 16:03:06.773][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:03:06.779][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:06.780][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:03:06.781][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-13 16:03:06.783][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-13 16:03:06.840][biodb::testThat]
biodb.INFO [2025-12-13 16:03:06.841][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-12-13 16:03:06.842][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:06.843][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:06.847][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-12-13 16:03:06.848][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-12-13 16:03:06.850][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-13 16:03:06.852][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:03:06.853][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:06.854][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:03:06.855][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-13 16:03:06.857][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2025-12-13 16:03:06.919][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:06.920][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:06.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:06.922][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:06.924][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:06.925][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:06.926][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:06.927][ef$get] fields variable is a list.
biodb.INFO [2025-12-13 16:03:06.929][biodb::testThat]
biodb.INFO [2025-12-13 16:03:06.930][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2025-12-13 16:03:06.931][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:06.932][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:06.936][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-12-13 16:03:06.937][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-12-13 16:03:06.939][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-13 16:03:06.940][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:03:06.942][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:06.943][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:03:06.944][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-13 16:03:06.945][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-13 16:03:07.007][biodb::testThat]
biodb.INFO [2025-12-13 16:03:07.008][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2025-12-13 16:03:07.009][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:07.010][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:07.014][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-12-13 16:03:07.016][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-12-13 16:03:07.018][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-13 16:03:07.019][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:03:07.020][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:07.022][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:03:07.023][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-13 16:03:07.024][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-13 16:03:07.081][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-13 16:03:07.082][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2025-12-13 16:03:07.083][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-13 16:03:07.084][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:07.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:07.086][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.225][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-12-13 16:03:07.231][biodb::testContext]
biodb.INFO [2025-12-13 16:03:07.233][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-13 16:03:07.234][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2025-12-13 16:03:07.235][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-13 16:03:07.236][biodb::testContext]
biodb.INFO [2025-12-13 16:03:07.238][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-13 16:03:07.240][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-12-13 16:03:07.245][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:07.246][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-13 16:03:07.247][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-13 16:03:07.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.252][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-13 16:03:07.253][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-13 16:03:07.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.257][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-13 16:03:07.259][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-13 16:03:07.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.263][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-13 16:03:07.264][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-13 16:03:07.265][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-13 16:03:07.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.270][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-13 16:03:07.271][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-13 16:03:07.272][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-13 16:03:07.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.277][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-13 16:03:07.278][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-13 16:03:07.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.282][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-13 16:03:07.284][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-13 16:03:07.285][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-13 16:03:07.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.290][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-13 16:03:07.291][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-13 16:03:07.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.296][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-13 16:03:07.297][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-13 16:03:07.299][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-13 16:03:07.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.303][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-13 16:03:07.304][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-13 16:03:07.306][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-13 16:03:07.307][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-13 16:03:07.308][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-13 16:03:07.309][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-13 16:03:07.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.314][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-13 16:03:07.315][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-13 16:03:07.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.319][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-13 16:03:07.321][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-13 16:03:07.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.325][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-13 16:03:07.327][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-13 16:03:07.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.331][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-13 16:03:07.333][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-13 16:03:07.334][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-13 16:03:07.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.339][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-13 16:03:07.340][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-13 16:03:07.350][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-13 16:03:07.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.355][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-13 16:03:07.356][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-13 16:03:07.358][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-13 16:03:07.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.362][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-13 16:03:07.364][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:07.366][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-13 16:03:07.367][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.368][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:07.369][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.371][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:07.372][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:07.373][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:07.374][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-13 16:03:07.376][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:07.377][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.378][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-13 16:03:07.379][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:07.380][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:07.382][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.383][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:07.383][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:03:07.383][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:03:07.383][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-13 16:03:07.383][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-13 16:03:07.385][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:07.386][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:07.388][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:07.389][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:07.390][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:07.392][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:07.393][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:07.395][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:07.396][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:07.397][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:07.399][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:07.400][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:07.402][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-13 16:03:07.405][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:07.406][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-13 16:03:07.408][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.409][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:07.411][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.412][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:07.413][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:07.415][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:07.416][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-13 16:03:07.418][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:07.419][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.421][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-13 16:03:07.422][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:07.424][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:07.425][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.427][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:07.427][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:03:07.427][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:03:07.427][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-13 16:03:07.427][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-13 16:03:07.428][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:07.430][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:07.431][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:07.432][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:07.434][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:07.435][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:07.436][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:07.438][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:07.439][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:07.441][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:07.442][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:07.443][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:07.445][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-13 16:03:07.448][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.449][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-13 16:03:07.451][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.452][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:07.454][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.455][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:07.456][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:07.458][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:07.459][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-13 16:03:07.461][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:07.462][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:07.464][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-13 16:03:07.465][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:07.467][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:07.468][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.470][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:07.471][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:07.473][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:07.474][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:07.475][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:07.477][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:07.478][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:07.479][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:07.481][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:07.482][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:07.484][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:07.485][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:07.487][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:07.488][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-13 16:03:07.491][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.493][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-13 16:03:07.494][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.496][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:07.498][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.499][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:07.501][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:07.502][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:07.504][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-13 16:03:07.505][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:07.507][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:07.509][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-13 16:03:07.510][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:07.512][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:07.513][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.515][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:07.517][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:07.518][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:07.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:07.521][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:07.523][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:07.524][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:07.525][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:07.527][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:07.528][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:07.530][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:07.531][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:07.532][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:07.534][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:07.536][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.589][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[2025-12-13 16:03:07.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.595][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[2025-12-13 16:03:07.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.621][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[2025-12-13 16:03:07.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.642][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-13 16:03:07.644][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-13 16:03:07.646][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-13 16:03:07.648][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-13 16:03:07.650][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-13 16:03:07.652][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-13 16:03:07.654][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-13 16:03:07.656][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-13 16:03:07.658][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-13 16:03:07.660][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-13 16:03:07.662][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-13 16:03:07.664][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-13 16:03:07.666][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-13 16:03:07.668][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-13 16:03:07.671][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-13 16:03:07.673][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-13 16:03:07.675][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-13 16:03:07.677][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-13 16:03:07.679][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-13 16:03:07.681][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-13 16:03:07.683][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-13 16:03:07.685][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-13 16:03:07.687][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-13 16:03:07.689][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-13 16:03:07.691][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-13 16:03:07.693][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-13 16:03:07.695][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-13 16:03:07.697][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-13 16:03:07.699][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-13 16:03:07.701][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-13 16:03:07.707][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-13 16:03:07.708][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-13 16:03:07.710][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-13 16:03:07.712][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-13 16:03:07.713][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-13 16:03:07.715][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-13 16:03:07.716][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-13 16:03:07.718][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-13 16:03:07.720][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-13 16:03:07.721][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-13 16:03:07.723][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-13 16:03:07.725][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-13 16:03:07.726][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-13 16:03:07.728][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-13 16:03:07.730][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-13 16:03:07.731][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-13 16:03:07.733][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-13 16:03:07.734][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-13 16:03:07.736][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-13 16:03:07.738][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-13 16:03:07.739][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-13 16:03:07.741][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-13 16:03:07.743][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-13 16:03:07.744][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-13 16:03:07.746][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-13 16:03:07.747][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-13 16:03:07.749][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-13 16:03:07.751][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-13 16:03:07.752][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-13 16:03:07.754][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-13 16:03:07.756][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-13 16:03:07.757][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-13 16:03:07.759][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-13 16:03:07.761][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-13 16:03:07.762][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-13 16:03:07.764][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-13 16:03:07.765][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-13 16:03:07.767][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-13 16:03:07.769][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-13 16:03:07.770][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-13 16:03:07.772][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-13 16:03:07.774][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-13 16:03:07.775][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-13 16:03:07.777][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-13 16:03:07.779][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-13 16:03:07.780][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-13 16:03:07.782][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-13 16:03:07.783][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-13 16:03:07.785][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-13 16:03:07.787][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-13 16:03:07.788][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-13 16:03:07.790][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-13 16:03:07.792][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-13 16:03:07.793][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-13 16:03:07.795][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-13 16:03:07.796][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:07.797][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.800][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.801][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[2025-12-13 16:03:07.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:07.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:07.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:07.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:07.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:07.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:07.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:07.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:07.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:07.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:07.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:07.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:07.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:07.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:07.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:07.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:07.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:07.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:07.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:07.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:07.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:07.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:07.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:07.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:07.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:07.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:07.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.899][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[2025-12-13 16:03:07.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:07.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:07.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:07.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:07.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:07.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:07.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:07.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:07.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:07.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:07.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:07.924][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-12-13 16:03:07.926][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-12-13 16:03:07.928][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.930][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-12-13 16:03:07.931][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.932][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:07.933][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.935][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:07.936][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.937][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:07.938][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-12-13 16:03:07.939][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:07.941][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.942][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-12-13 16:03:07.943][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:07.944][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-12-13 16:03:07.944][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-12-13 16:03:07.946][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:07.947][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:07.948][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-13 16:03:07.949][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:07.950][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:07.952][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:07.953][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:07.954][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:07.955][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:07.956][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-13 16:03:07.956][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-12-13 16:03:07.957][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:07.958][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:07.960][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.961][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:07.962][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-12-13 16:03:07.965][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.966][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-12-13 16:03:07.967][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.968][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:07.970][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.971][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:07.972][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.973][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:07.974][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-13 16:03:07.976][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:07.977][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.978][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-12-13 16:03:07.979][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:07.981][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-12-13 16:03:07.981][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-12-13 16:03:07.981][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-12-13 16:03:07.981][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-12-13 16:03:07.981][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-12-13 16:03:07.981][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-12-13 16:03:07.982][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:07.983][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:07.984][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-13 16:03:07.986][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:07.987][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:07.988][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:07.989][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:07.990][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:07.991][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:07.992][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:07.992][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-13 16:03:07.994][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:07.995][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:07.996][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:07.997][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:07.999][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-12-13 16:03:08.001][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:08.002][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-12-13 16:03:08.003][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:08.005][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:08.006][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:08.007][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:08.008][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:08.010][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:08.011][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-13 16:03:08.012][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:08.013][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:08.015][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-12-13 16:03:08.016][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:08.017][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-13 16:03:08.017][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:08.017][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:08.017][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:08.017][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:08.017][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:08.017][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:08.017][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:08.017][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:08.017][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:08.017][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-12-13 16:03:08.017][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:08.017][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:08.017][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-13 16:03:08.019][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:08.020][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:08.020][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:03:08.020][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:03:08.021][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-13 16:03:08.022][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:08.023][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:08.025][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:08.026][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:08.027][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:08.028][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:08.029][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:08.029][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-13 16:03:08.029][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-13 16:03:08.031][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:08.032][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:08.033][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:08.034][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-13 16:03:08.036][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-12-13 16:03:08.038][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:08.039][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-12-13 16:03:08.040][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:08.042][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:08.043][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:08.044][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:08.045][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:08.047][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:08.048][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-13 16:03:08.049][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:08.050][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:08.052][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-12-13 16:03:08.053][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:08.054][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-12-13 16:03:08.054][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-13 16:03:08.055][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:08.057][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:08.058][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-13 16:03:08.059][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:08.060][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:08.061][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:08.062][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:08.064][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:08.065][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:08.066][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:08.066][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-13 16:03:08.066][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-13 16:03:08.067][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:08.068][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:08.070][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:08.071][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-13 16:03:08.072][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-12-13 16:03:08.074][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-13 16:03:08.076][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-13 16:03:08.078][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-12-13 16:03:08.080][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-13 16:03:08.082][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-12-13 16:03:08.088][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2025-12-13 16:03:08.097][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2025-12-13 16:03:08.102][biodb::testThat]
biodb.INFO [2025-12-13 16:03:08.104][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-13 16:03:08.105][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:08.106][biodb::testThat]
biodb.TRACE[2025-12-13 16:03:08.110][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2025-12-13 16:03:08.112][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-12-13 16:03:08.121][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-12-13 16:03:08.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-13 16:03:08.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:08.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:08.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:08.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:08.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:08.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-13 16:03:08.138][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.140][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.142][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.148][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:08.150][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:08.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.152][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.154][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:08.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:08.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.159][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-13 16:03:08.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-13 16:03:08.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.163][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-13 16:03:08.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-13 16:03:08.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.173][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-13 16:03:08.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-13 16:03:08.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-13 16:03:08.206][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2025-12-13 16:03:08.209][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-13 16:03:08.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:03:08.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.214][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-13 16:03:08.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-13 16:03:08.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.219][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:03:08.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-13 16:03:08.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.223][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:03:08.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:03:08.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.228][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:03:08.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:03:08.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.233][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-13 16:03:08.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-13 16:03:08.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.238][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-13 16:03:08.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-13 16:03:08.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.253][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-13 16:03:08.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-13 16:03:08.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.296][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-13 16:03:08.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-13 16:03:08.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.301][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-13 16:03:08.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-13 16:03:08.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.307][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-13 16:03:08.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-13 16:03:08.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.335][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.336][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.338][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.355][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:08.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:08.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.360][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:08.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:08.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.365][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:08.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:08.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.371][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:08.372][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:08.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.375][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.376][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:08.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:08.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.392][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:08.394][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:08.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.396][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:08.403][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:08.405][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:03:08.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:08.407][ef$get] fields variable is a list.
biodb.INFO [2025-12-13 16:03:08.418][biodb::testThat]
biodb.INFO [2025-12-13 16:03:08.419][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-13 16:03:08.421][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:08.422][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:08.425][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-12-13 16:03:08.429][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-12-13 16:03:08.431][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-13 16:03:08.432][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:03:08.434][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:08.435][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:03:08.436][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-13 16:03:08.438][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-12-13 16:03:08.495][biodb::testThat]
biodb.INFO [2025-12-13 16:03:08.496][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-13 16:03:08.497][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:08.499][biodb::testThat]
biodb.INFO [2025-12-13 16:03:08.507][biodb::testThat]
biodb.INFO [2025-12-13 16:03:08.508][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-13 16:03:08.509][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:08.510][biodb::testThat]
biodb.WARN [2025-12-13 16:03:08.514][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-12-13 16:03:08.519][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-12-13 16:03:08.531][biodb::testThat]
biodb.INFO [2025-12-13 16:03:08.533][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-13 16:03:08.534][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:08.535][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:08.540][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-12-13 16:03:08.542][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-12-13 16:03:08.543][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-13 16:03:08.545][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-12-13 16:03:08.546][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:08.547][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-13 16:03:08.549][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-13 16:03:08.550][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-12-13 16:03:08.612][biodb::testThat]
biodb.INFO [2025-12-13 16:03:08.613][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-13 16:03:08.614][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:08.615][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-12-13 16:03:08.672][biodb::testThat]
biodb.INFO [2025-12-13 16:03:08.674][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-13 16:03:08.675][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:08.676][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-12-13 16:03:08.733][biodb::testThat]
biodb.INFO [2025-12-13 16:03:08.735][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-13 16:03:08.736][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:08.737][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-12-13 16:03:08.796][biodb::testThat]
biodb.INFO [2025-12-13 16:03:08.797][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-13 16:03:08.798][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:08.799][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-12-13 16:03:08.858][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-13 16:03:08.860][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2025-12-13 16:03:08.861][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-13 16:03:08.862][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:08.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:08.864][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:08.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:08.867][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:08.868][FUN] Functions in observer 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)