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"	4890
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4680
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: 2026-02-21 16:01:21 -0500 (Sat, 21 Feb 2026)

EndedAt: 2026-02-21 16:02:41 -0500 (Sat, 21 Feb 2026)

EllapsedTime: 79.2 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"
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Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNcbi")
Loading required package: biodbNcbi
biodb.INFO [2026-02-21 16:02:28.410][biodb::testContext]
biodb.INFO [2026-02-21 16:02:28.414][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:02:28.415][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2026-02-21 16:02:28.417][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:02:28.418][biodb::testContext]
biodb.INFO [2026-02-21 16:02:28.424][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:02:28.426][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-21 16:02:28.433][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:28.435][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-21 16:02:28.436][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-21 16:02:28.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.441][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-21 16:02:28.464][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-21 16:02:28.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.469][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-21 16:02:28.470][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-21 16:02:28.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.475][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-21 16:02:28.476][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-21 16:02:28.477][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-21 16:02:28.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.481][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.DEBUG[2026-02-21 16:02:28.482][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-21 16:02:28.483][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-21 16:02:28.485][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-21 16:02:28.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.489][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-21 16:02:28.490][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-21 16:02:28.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.494][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.DEBUG[2026-02-21 16:02:28.495][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-21 16:02:28.496][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-21 16:02:28.497][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-21 16:02:28.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.502][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-21 16:02:28.503][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-21 16:02:28.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.508][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-21 16:02:28.509][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-21 16:02:28.510][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-21 16:02:28.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.515][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:02:28.516][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-21 16:02:28.517][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-21 16:02:28.519][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-21 16:02:28.520][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-21 16:02:28.521][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-21 16:02:28.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.524][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[2026-02-21 16:02:28.526][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-21 16:02:28.527][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-21 16:02:28.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.532][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-21 16:02:28.533][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-21 16:02:28.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.537][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-21 16:02:28.539][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-21 16:02:28.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.543][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-21 16:02:28.545][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-21 16:02:28.546][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-21 16:02:28.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.550][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:02:28.552][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-21 16:02:28.562][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-21 16:02:28.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.567][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-21 16:02:28.569][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-21 16:02:28.570][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-21 16:02:28.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.574][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[2026-02-21 16:02:28.578][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-21 16:02:28.628][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:28.650][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-21 16:02:28.651][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:28.652][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:28.653][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:28.655][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:28.656][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:28.657][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:28.658][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:02:28.660][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:28.661][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:28.662][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-21 16:02:28.664][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:28.665][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:28.666][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:28.667][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:28.667][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:28.667][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:28.667][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:02:28.667][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:02:28.669][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:28.670][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:28.671][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:28.672][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:28.673][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:28.675][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:28.676][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:28.677][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:28.678][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:28.679][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:28.681][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:28.682][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:28.683][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-21 16:02:28.686][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:28.687][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:02:28.688][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:28.690][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:28.691][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:28.692][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:28.693][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:28.695][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:28.696][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:02:28.697][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:28.698][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:28.700][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-21 16:02:28.701][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:28.702][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:28.703][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:28.705][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:28.705][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:28.705][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:28.705][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:02:28.705][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:02:28.706][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:28.707][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:28.708][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:28.709][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:28.711][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:28.712][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:28.713][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:28.714][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:28.715][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:28.716][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:28.718][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:28.719][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:28.720][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-21 16:02:28.723][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:28.724][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-21 16:02:28.725][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:28.726][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:28.728][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:28.729][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:28.730][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:28.731][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:28.733][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:02:28.734][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:28.735][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:28.736][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-21 16:02:28.738][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:28.739][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:28.740][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:28.741][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:28.743][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:28.744][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:28.745][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:28.746][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:28.747][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:28.748][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:28.750][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:28.751][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:28.752][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:28.753][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:28.754][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:28.756][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:28.757][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-21 16:02:28.759][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:28.761][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:02:28.762][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:28.763][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:28.764][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:28.766][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:28.767][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:28.768][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:28.769][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:02:28.771][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:28.772][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:28.773][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-21 16:02:28.774][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:28.776][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:28.777][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:28.778][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:28.780][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:28.781][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:28.782][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:28.783][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:28.785][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:28.786][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:28.787][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:28.788][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:28.790][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:28.791][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:28.792][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:28.793][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:28.797][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:28.799][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.800][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[2026-02-21 16:02:28.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:28.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:28.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:28.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:28.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.811][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[2026-02-21 16:02:28.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:28.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:28.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:28.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:28.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.823][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[2026-02-21 16:02:28.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:28.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:28.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:28.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:28.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:28.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:28.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:28.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:28.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.846][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[2026-02-21 16:02:28.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:28.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:28.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:28.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:28.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:28.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:28.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:28.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:28.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:28.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:28.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:28.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:28.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:28.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:28.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.890][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[2026-02-21 16:02:28.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:28.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:28.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:28.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:28.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:28.897][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-21 16:02:28.902][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-21 16:02:28.903][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-21 16:02:28.905][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-21 16:02:28.907][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-21 16:02:28.909][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-21 16:02:28.910][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-21 16:02:28.912][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-21 16:02:28.914][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-21 16:02:28.915][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-21 16:02:28.917][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-21 16:02:28.919][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-21 16:02:28.920][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-21 16:02:28.922][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-21 16:02:28.924][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-21 16:02:28.926][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-21 16:02:28.927][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-21 16:02:28.929][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-21 16:02:28.931][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-21 16:02:28.932][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-21 16:02:28.934][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-21 16:02:28.936][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-21 16:02:28.938][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-21 16:02:28.939][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-21 16:02:28.941][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-21 16:02:28.943][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-21 16:02:28.944][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-21 16:02:28.946][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-21 16:02:28.948][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-21 16:02:28.950][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-21 16:02:28.952][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-21 16:02:28.953][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-21 16:02:28.955][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-21 16:02:28.957][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-21 16:02:28.958][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-21 16:02:28.960][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-21 16:02:28.962][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-21 16:02:28.964][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-21 16:02:28.966][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-21 16:02:28.967][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-21 16:02:28.969][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-21 16:02:28.971][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-21 16:02:28.972][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-21 16:02:28.974][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-21 16:02:28.976][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-21 16:02:28.977][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-21 16:02:28.979][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-21 16:02:28.981][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-21 16:02:28.983][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-21 16:02:28.984][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-21 16:02:28.986][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-21 16:02:28.988][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-21 16:02:28.989][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-21 16:02:28.991][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-21 16:02:28.993][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-21 16:02:28.995][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-21 16:02:28.996][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-21 16:02:28.998][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-21 16:02:29.000][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-21 16:02:29.002][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-21 16:02:29.003][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-21 16:02:29.005][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-21 16:02:29.007][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-21 16:02:29.008][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-21 16:02:29.010][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-21 16:02:29.012][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-21 16:02:29.013][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-21 16:02:29.015][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-21 16:02:29.017][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-21 16:02:29.019][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-21 16:02:29.020][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-21 16:02:29.022][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-21 16:02:29.024][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-21 16:02:29.026][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-21 16:02:29.027][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-21 16:02:29.029][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-21 16:02:29.031][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-21 16:02:29.033][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-21 16:02:29.034][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-21 16:02:29.036][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-21 16:02:29.038][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-21 16:02:29.039][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-21 16:02:29.041][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-21 16:02:29.048][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-21 16:02:29.051][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:02:29.054][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:29.055][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:29.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:29.057][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:29.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:29.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:29.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:29.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:29.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:29.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:29.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:29.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:29.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:29.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:29.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:29.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:29.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:29.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:29.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:29.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:29.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:29.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:29.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:29.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:29.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:29.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:29.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:29.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:29.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:29.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:29.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:29.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:29.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:29.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:29.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:29.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:29.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:29.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:29.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:29.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:29.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:29.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:29.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:29.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:29.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:29.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:29.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:29.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:29.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:29.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:29.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:29.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:29.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:29.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:29.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:29.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:29.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:29.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:29.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:29.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:29.125][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[2026-02-21 16:02:29.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:29.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:29.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:29.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:29.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:29.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:29.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:29.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:29.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:29.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:29.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:29.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:29.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:29.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:29.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:29.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:29.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:29.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:29.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:29.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:29.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:29.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:29.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:29.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:29.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:29.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:29.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:29.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:29.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:29.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:29.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:29.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:29.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:29.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:29.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:29.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:29.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:29.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:29.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:29.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:29.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:29.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:29.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:29.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:29.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:29.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:29.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:29.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:29.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:29.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:29.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:29.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:29.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:29.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:29.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:29.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:29.195][bdb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-02-21 16:02:29.208][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-02-21 16:02:29.211][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.212][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-02-21 16:02:29.213][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.215][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:29.216][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.217][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:29.218][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.220][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:29.221][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-02-21 16:02:29.222][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:29.223][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.225][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-02-21 16:02:29.226][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:29.227][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-02-21 16:02:29.227][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-02-21 16:02:29.228][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:29.230][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:29.231][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-21 16:02:29.232][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:29.233][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:29.234][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:29.236][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:29.237][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:29.238][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:29.239][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-21 16:02:29.239][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-02-21 16:02:29.240][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:29.241][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:29.243][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.244][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:29.245][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-02-21 16:02:29.248][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.249][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-02-21 16:02:29.250][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.251][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:29.253][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.254][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:29.255][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.256][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:29.257][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-21 16:02:29.259][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:29.260][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.261][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-02-21 16:02:29.262][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:29.264][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-02-21 16:02:29.264][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-02-21 16:02:29.264][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-02-21 16:02:29.264][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-02-21 16:02:29.264][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-02-21 16:02:29.264][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-02-21 16:02:29.265][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:29.266][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:29.268][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-21 16:02:29.269][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:29.270][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:29.271][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:29.272][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:29.273][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:29.275][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:29.276][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:29.276][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-21 16:02:29.277][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:29.278][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:29.279][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.281][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:29.282][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-02-21 16:02:29.284][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:29.286][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-02-21 16:02:29.287][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.288][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:29.289][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.291][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:29.292][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.293][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:29.294][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-21 16:02:29.296][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:29.297][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.298][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-02-21 16:02:29.299][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:29.301][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-21 16:02:29.301][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:29.301][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:29.301][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:29.301][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:29.301][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:29.301][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:29.301][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:29.301][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:29.301][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:29.301][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-02-21 16:02:29.301][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:29.301][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:29.301][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:29.302][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:29.304][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:29.304][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:29.304][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:29.305][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-21 16:02:29.306][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:29.307][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:29.309][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:29.310][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:29.311][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:29.312][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:29.314][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:29.314][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-21 16:02:29.314][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-21 16:02:29.315][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:29.316][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:29.318][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.319][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-21 16:02:29.321][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-02-21 16:02:29.323][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.324][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-02-21 16:02:29.325][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.327][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:29.328][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.329][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:29.331][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.332][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:29.333][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-21 16:02:29.334][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:29.336][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.337][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-02-21 16:02:29.338][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:29.339][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-02-21 16:02:29.339][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-21 16:02:29.341][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:29.342][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:29.343][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-21 16:02:29.345][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:29.346][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:29.347][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:29.348][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:29.349][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:29.350][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:29.352][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:29.352][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-21 16:02:29.352][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-21 16:02:29.353][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:29.354][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:29.356][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:29.357][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-21 16:02:29.365][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-02-21 16:02:29.367][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-21 16:02:29.368][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-21 16:02:29.370][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-02-21 16:02:29.372][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-21 16:02:29.374][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-02-21 16:02:29.395][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2026-02-21 16:02:29.414][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2026-02-21 16:02:29.423][biodb::testThat]
biodb.INFO [2026-02-21 16:02:29.424][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-21 16:02:29.426][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:29.427][biodb::testThat]
biodb.TRACE[2026-02-21 16:02:29.431][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2026-02-21 16:02:29.433][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2026-02-21 16:02:29.437][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2026-02-21 16:02:29.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-21 16:02:29.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:29.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:29.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:29.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:29.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:29.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-21 16:02:29.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.509][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-02-21 16:02:29.526][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:29.528][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.529][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.566][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-02-21 16:02:29.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:29.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.571][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:29.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:29.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.576][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:29.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:29.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.587][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:29.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:29.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-21 16:02:29.682][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2026-02-21 16:02:29.685][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-21 16:02:29.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:29.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.691][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-21 16:02:29.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:29.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.728][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:02:29.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:02:29.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.733][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:02:29.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:02:29.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.738][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-21 16:02:29.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-21 16:02:29.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.743][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-21 16:02:29.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-21 16:02:29.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.772][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:29.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:29.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.818][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:29.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:29.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.823][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:29.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:29.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.828][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:29.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:29.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.858][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.860][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.861][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.862][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.880][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-02-21 16:02:29.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:29.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.889][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-21 16:02:29.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:29.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.894][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-21 16:02:29.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:29.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.899][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-02-21 16:02:29.901][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:29.902][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.903][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.904][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-02-21 16:02:29.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:29.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.920][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-21 16:02:29.921][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:29.922][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.924][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.930][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:29.931][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:29.932][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:29.934][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:29.956][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2026-02-21 16:02:30.004][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2026-02-21 16:02:30.005][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2026-02-21 16:02:30.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-21 16:02:30.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:30.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:30.015][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:30.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:30.018][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:30.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-21 16:02:30.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.062][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-02-21 16:02:30.063][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:30.064][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.066][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.067][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-02-21 16:02:30.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:30.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.072][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:30.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:30.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.077][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:30.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:30.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.124][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:30.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:30.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-21 16:02:30.159][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2026-02-21 16:02:30.186][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-21 16:02:30.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:30.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.191][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-21 16:02:30.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:30.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.196][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:02:30.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:02:30.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.201][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:02:30.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:02:30.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.206][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-21 16:02:30.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-21 16:02:30.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.211][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-21 16:02:30.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-21 16:02:30.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.227][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:30.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:30.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.270][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:30.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:30.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.275][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:30.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:30.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.281][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:30.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:30.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.324][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.325][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.327][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.328][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.349][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-02-21 16:02:30.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:30.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.355][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-21 16:02:30.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:30.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.360][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-21 16:02:30.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:30.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.365][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-02-21 16:02:30.367][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:30.368][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.369][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.370][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-02-21 16:02:30.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:30.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.386][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-21 16:02:30.388][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:30.389][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.390][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:30.397][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:30.399][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:30.400][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:30.402][ef$get] fields variable is a list.
biodb.INFO [2026-02-21 16:02:30.413][biodb::testThat]
biodb.INFO [2026-02-21 16:02:30.415][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-21 16:02:30.416][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:30.417][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:30.421][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2026-02-21 16:02:30.426][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2026-02-21 16:02:30.430][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-02-21 16:02:30.432][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:30.433][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-21 16:02:30.434][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:30.436][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-02-21 16:02:30.621][biodb::testThat]
biodb.INFO [2026-02-21 16:02:30.623][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-21 16:02:30.624][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:30.625][biodb::testThat]
biodb.INFO [2026-02-21 16:02:30.633][biodb::testThat]
biodb.INFO [2026-02-21 16:02:30.635][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-21 16:02:30.636][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:30.637][biodb::testThat]
biodb.WARN [2026-02-21 16:02:30.659][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-02-21 16:02:30.684][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-02-21 16:02:30.695][biodb::testThat]
biodb.INFO [2026-02-21 16:02:30.697][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-21 16:02:30.698][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:30.699][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:30.723][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2026-02-21 16:02:30.791][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2026-02-21 16:02:30.831][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-02-21 16:02:30.832][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:30.833][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-21 16:02:30.835][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:30.836][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-02-21 16:02:30.931][biodb::testThat]
biodb.INFO [2026-02-21 16:02:30.933][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-21 16:02:30.934][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:30.935][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-02-21 16:02:30.993][biodb::testThat]
biodb.INFO [2026-02-21 16:02:30.994][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-21 16:02:30.995][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:30.996][biodb::testThat]
biodb.INFO [2026-02-21 16:02:31.007][biodb::testThat]
biodb.INFO [2026-02-21 16:02:31.008][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-21 16:02:31.009][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:31.010][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-02-21 16:02:31.069][biodb::testThat]
biodb.INFO [2026-02-21 16:02:31.070][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-21 16:02:31.072][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:31.073][biodb::testThat]
biodb.INFO [2026-02-21 16:02:31.081][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-21 16:02:31.083][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2026-02-21 16:02:31.084][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-21 16:02:31.085][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:31.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:31.087][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.089][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-02-21 16:02:31.110][biodb::testContext]
biodb.INFO [2026-02-21 16:02:31.111][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:02:31.112][biodb::testContext] Test context - Gene long tests
biodb.INFO [2026-02-21 16:02:31.114][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:02:31.115][biodb::testContext]
biodb.INFO [2026-02-21 16:02:31.117][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:02:31.120][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-21 16:02:31.124][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:31.126][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-21 16:02:31.127][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-21 16:02:31.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.132][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-21 16:02:31.133][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-21 16:02:31.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.138][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-21 16:02:31.139][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-21 16:02:31.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.144][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-21 16:02:31.145][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-21 16:02:31.146][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-21 16:02:31.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.151][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-21 16:02:31.152][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-21 16:02:31.154][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-21 16:02:31.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.159][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-21 16:02:31.160][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-21 16:02:31.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.165][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-21 16:02:31.166][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-21 16:02:31.168][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-21 16:02:31.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.171][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[2026-02-21 16:02:31.173][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-21 16:02:31.174][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-21 16:02:31.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.179][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-21 16:02:31.181][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-21 16:02:31.182][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-21 16:02:31.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.187][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:02:31.188][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-21 16:02:31.189][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-21 16:02:31.190][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-21 16:02:31.192][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-21 16:02:31.193][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-21 16:02:31.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.198][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-21 16:02:31.199][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-21 16:02:31.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.203][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[2026-02-21 16:02:31.204][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-21 16:02:31.205][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-21 16:02:31.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.210][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-21 16:02:31.211][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-21 16:02:31.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.216][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-21 16:02:31.217][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-21 16:02:31.219][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-21 16:02:31.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.223][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:02:31.225][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-21 16:02:31.235][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-21 16:02:31.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.240][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-21 16:02:31.241][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-21 16:02:31.243][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-21 16:02:31.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.247][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-21 16:02:31.250][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:31.251][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-21 16:02:31.252][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.253][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:31.255][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.256][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.257][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:31.258][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.260][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:02:31.261][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:31.262][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.263][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-21 16:02:31.265][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:31.266][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:31.267][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.269][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:31.269][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:31.269][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:31.269][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:02:31.269][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:02:31.270][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:31.271][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:31.272][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:31.274][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:31.275][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:31.276][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:31.277][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.279][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:31.280][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:31.281][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:31.282][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:31.283][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:31.285][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-21 16:02:31.287][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:31.289][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:02:31.290][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.291][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:31.292][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.294][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.295][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:31.296][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.297][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:02:31.299][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:31.300][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.301][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-21 16:02:31.303][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:31.304][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:31.305][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.306][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:31.306][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:31.306][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:31.306][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:02:31.306][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:02:31.308][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:31.309][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:31.310][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:31.311][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:31.313][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:31.318][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:31.320][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.321][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:31.322][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:31.323][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:31.324][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:31.326][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:31.327][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-21 16:02:31.329][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.331][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-21 16:02:31.332][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.333][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:31.334][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.336][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.337][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:31.338][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.339][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:02:31.341][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:31.342][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:31.343][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-21 16:02:31.344][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:31.346][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:31.347][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.348][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:31.349][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:31.351][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:31.352][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:31.353][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:31.354][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:31.355][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:31.356][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.358][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:31.359][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:31.360][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:31.361][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:31.363][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:31.364][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-21 16:02:31.366][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.368][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:02:31.369][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.370][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:31.371][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.372][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.374][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:31.375][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.376][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:02:31.377][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:31.379][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:31.380][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-21 16:02:31.381][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:31.382][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:31.384][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.385][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:31.386][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:31.387][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:31.389][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:31.390][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:31.391][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:31.392][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:31.393][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.395][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:31.396][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:31.397][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:31.398][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:31.399][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:31.401][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:31.402][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.506][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-21 16:02:31.508][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-21 16:02:31.510][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-21 16:02:31.512][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-21 16:02:31.515][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-21 16:02:31.516][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-21 16:02:31.518][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-21 16:02:31.520][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-21 16:02:31.528][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-21 16:02:31.532][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-21 16:02:31.535][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-21 16:02:31.537][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-21 16:02:31.539][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-21 16:02:31.541][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-21 16:02:31.543][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-21 16:02:31.546][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-21 16:02:31.548][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-21 16:02:31.550][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-21 16:02:31.552][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-21 16:02:31.554][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-21 16:02:31.556][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-21 16:02:31.558][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-21 16:02:31.560][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-21 16:02:31.562][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-21 16:02:31.564][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-21 16:02:31.566][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-21 16:02:31.568][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-21 16:02:31.569][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-21 16:02:31.572][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-21 16:02:31.573][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-21 16:02:31.575][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-21 16:02:31.577][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-21 16:02:31.579][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-21 16:02:31.581][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-21 16:02:31.583][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-21 16:02:31.584][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-21 16:02:31.586][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-21 16:02:31.588][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-21 16:02:31.589][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-21 16:02:31.591][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-21 16:02:31.593][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-21 16:02:31.595][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-21 16:02:31.596][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-21 16:02:31.598][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-21 16:02:31.600][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-21 16:02:31.602][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-21 16:02:31.603][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-21 16:02:31.605][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-21 16:02:31.607][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-21 16:02:31.608][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-21 16:02:31.610][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-21 16:02:31.612][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-21 16:02:31.614][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-21 16:02:31.615][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-21 16:02:31.617][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-21 16:02:31.619][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-21 16:02:31.620][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-21 16:02:31.622][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-21 16:02:31.624][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-21 16:02:31.626][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-21 16:02:31.627][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-21 16:02:31.629][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-21 16:02:31.631][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-21 16:02:31.632][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-21 16:02:31.634][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-21 16:02:31.636][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-21 16:02:31.637][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-21 16:02:31.639][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-21 16:02:31.641][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-21 16:02:31.643][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-21 16:02:31.645][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-21 16:02:31.646][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-21 16:02:31.648][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-21 16:02:31.650][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-21 16:02:31.652][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-21 16:02:31.654][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-21 16:02:31.655][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-21 16:02:31.658][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-21 16:02:31.661][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-21 16:02:31.664][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-21 16:02:31.666][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-21 16:02:31.668][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-21 16:02:31.670][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-21 16:02:31.672][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-21 16:02:31.674][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:02:31.675][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:31.676][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.678][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:31.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:31.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:31.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:31.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:31.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:31.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:31.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:31.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:31.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:31.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:31.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:31.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:31.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:31.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:31.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:31.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:31.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:31.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:31.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:31.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:31.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:31.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:31.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:31.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:31.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:31.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:31.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:31.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:31.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:31.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:31.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:31.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:31.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:31.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:31.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:31.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:31.811][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[2026-02-21 16:02:31.814][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-02-21 16:02:31.817][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-02-21 16:02:31.820][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.821][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-02-21 16:02:31.822][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.824][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:31.825][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.826][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.827][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.829][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.830][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-02-21 16:02:31.831][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:31.832][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.834][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-02-21 16:02:31.835][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:31.836][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-02-21 16:02:31.836][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-02-21 16:02:31.837][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:31.839][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:31.840][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-21 16:02:31.841][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:31.842][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:31.843][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:31.844][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:31.846][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:31.847][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.848][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-21 16:02:31.848][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-02-21 16:02:31.849][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:31.851][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:31.852][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.853][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:31.855][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-02-21 16:02:31.857][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.860][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-02-21 16:02:31.862][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.863][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:31.864][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.866][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.867][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.869][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.872][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-21 16:02:31.874][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:31.876][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.878][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-02-21 16:02:31.880][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:31.881][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-02-21 16:02:31.881][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-02-21 16:02:31.881][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-02-21 16:02:31.881][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-02-21 16:02:31.881][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-02-21 16:02:31.881][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-02-21 16:02:31.883][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:31.884][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:31.886][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-21 16:02:31.887][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:31.888][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:31.889][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:31.890][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:31.891][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:31.893][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.894][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:31.894][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-21 16:02:31.895][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:31.896][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:31.897][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.899][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:31.900][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-02-21 16:02:31.903][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:31.904][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-02-21 16:02:31.905][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.906][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:31.908][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.909][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.910][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.911][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.913][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-21 16:02:31.914][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:31.915][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.916][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-02-21 16:02:31.918][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:31.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-21 16:02:31.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:31.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:31.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:31.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:31.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:31.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:31.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:31.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:31.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:31.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-02-21 16:02:31.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:31.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:31.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:31.921][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:31.922][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:31.922][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:31.922][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:31.923][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-21 16:02:31.924][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:31.926][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:31.927][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:31.928][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:31.929][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:31.930][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.936][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:31.936][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-21 16:02:31.936][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-21 16:02:31.937][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:31.938][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:31.940][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.941][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-21 16:02:31.943][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-02-21 16:02:31.945][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.946][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-02-21 16:02:31.947][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.949][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:31.950][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.951][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.952][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.954][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.955][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-21 16:02:31.956][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:31.957][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.959][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-02-21 16:02:31.960][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:31.961][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-02-21 16:02:31.961][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-21 16:02:31.962][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:31.964][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:31.965][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-21 16:02:31.966][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:31.967][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:31.968][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:31.969][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:31.970][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:31.972][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:31.973][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:31.973][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-21 16:02:31.973][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-21 16:02:31.974][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:31.975][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:31.976][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:31.978][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-21 16:02:31.979][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-02-21 16:02:31.981][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-21 16:02:31.983][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-21 16:02:31.985][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-02-21 16:02:31.987][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-21 16:02:31.988][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-02-21 16:02:31.997][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2026-02-21 16:02:32.036][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2026-02-21 16:02:32.041][biodb::testThat]
biodb.INFO [2026-02-21 16:02:32.043][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-21 16:02:32.044][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:32.045][biodb::testThat]
biodb.TRACE[2026-02-21 16:02:32.051][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2026-02-21 16:02:32.053][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2026-02-21 16:02:32.057][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2026-02-21 16:02:32.059][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-21 16:02:32.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:32.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:32.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:32.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:32.071][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:32.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-21 16:02:32.086][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:32.088][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:32.089][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.090][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:32.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:32.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.097][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:32.099][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:32.100][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.101][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.103][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:32.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:32.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.108][ef$get] Asked field names are: location.
biodb.TRACE[2026-02-21 16:02:32.110][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2026-02-21 16:02:32.111][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.112][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.114][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2026-02-21 16:02:32.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2026-02-21 16:02:32.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.119][ef$get] Asked field names are: symbol.
biodb.TRACE[2026-02-21 16:02:32.120][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2026-02-21 16:02:32.122][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.123][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.125][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2026-02-21 16:02:32.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2026-02-21 16:02:32.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.130][ef$get] Asked field names are: synonyms.
biodb.TRACE[2026-02-21 16:02:32.131][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:32.132][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.133][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.136][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2026-02-21 16:02:32.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:32.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.141][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2026-02-21 16:02:32.148][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2026-02-21 16:02:32.149][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.150][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.153][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2026-02-21 16:02:32.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2026-02-21 16:02:32.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.163][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:32.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:32.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.168][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-02-21 16:02:32.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-02-21 16:02:32.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.173][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-02-21 16:02:32.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-02-21 16:02:32.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:32.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:32.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.183][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-02-21 16:02:32.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-02-21 16:02:32.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:32.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:32.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:32.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:32.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:32.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:32.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:32.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:32.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:32.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:32.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:32.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:32.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-21 16:02:32.218][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2026-02-21 16:02:32.220][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-21 16:02:32.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:32.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.225][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-21 16:02:32.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:32.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.230][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:32.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:32.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.235][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:32.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:32.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:32.240][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:32.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:32.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-21 16:02:32.245][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2026-02-21 16:02:32.284][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2026-02-21 16:02:32.304][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2026-02-21 16:02:32.305][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2026-02-21 16:02:32.309][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2026-02-21 16:02:32.311][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-02-21 16:02:32.313][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:32.314][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-21 16:02:32.315][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:32.316][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-21 16:02:32.378][biodb::testThat]
biodb.INFO [2026-02-21 16:02:32.380][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-21 16:02:32.381][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:32.382][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:32.385][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2026-02-21 16:02:32.386][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2026-02-21 16:02:32.388][cch$loadContents] Load 8 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-02-21 16:02:32.390][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:32.391][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:32.392][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:32.393][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-21 16:02:32.394][private$retrieveContents] Get entry content(s) for 8 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-21 16:02:32.486][biodb::testThat]
biodb.INFO [2026-02-21 16:02:32.489][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-21 16:02:32.491][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:32.493][biodb::testThat]
biodb.TRACE[2026-02-21 16:02:32.501][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:32.503][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:32.506][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:32.508][ef$get] fields variable is a list.
biodb.DEBUG[2026-02-21 16:02:32.510][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2026-02-21 16:02:32.530][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-02-21 16:02:32.620][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-02-21 16:02:32.622][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-02-21 16:02:32.624][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:32.625][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:32.626][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:32.627][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-21 16:02:32.651][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-21 16:02:32.740][biodb::testThat]
biodb.INFO [2026-02-21 16:02:32.742][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-21 16:02:32.743][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:32.744][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:32.754][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-02-21 16:02:32.756][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-02-21 16:02:32.758][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-02-21 16:02:32.759][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:32.761][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:32.762][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:32.763][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-21 16:02:32.765][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-21 16:02:32.825][biodb::testThat]
biodb.INFO [2026-02-21 16:02:32.826][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-21 16:02:32.828][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:32.829][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:32.835][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-02-21 16:02:32.836][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-02-21 16:02:32.838][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-02-21 16:02:32.839][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:32.841][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:32.842][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:32.843][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-21 16:02:32.845][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-21 16:02:32.905][biodb::testThat]
biodb.INFO [2026-02-21 16:02:32.906][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-21 16:02:32.912][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:32.913][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-21 16:02:32.971][biodb::testThat]
biodb.INFO [2026-02-21 16:02:32.972][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-21 16:02:32.973][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:32.975][biodb::testThat]
biodb.INFO [2026-02-21 16:02:32.985][biodb::testThat]
biodb.INFO [2026-02-21 16:02:32.986][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-21 16:02:32.987][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:32.988][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-21 16:02:33.048][biodb::testThat]
biodb.INFO [2026-02-21 16:02:33.049][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-21 16:02:33.051][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:33.052][biodb::testThat]
biodb.INFO [2026-02-21 16:02:33.060][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-21 16:02:33.062][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2026-02-21 16:02:33.063][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2026-02-21 16:02:33.064][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-21 16:02:33.065][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:33.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:33.067][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.070][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-02-21 16:02:33.076][biodb::testContext]
biodb.INFO [2026-02-21 16:02:33.077][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:02:33.078][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2026-02-21 16:02:33.080][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:02:33.086][biodb::testContext]
biodb.INFO [2026-02-21 16:02:33.089][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:02:33.091][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-21 16:02:33.095][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:33.097][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-21 16:02:33.098][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-21 16:02:33.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.103][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-21 16:02:33.104][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-21 16:02:33.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.109][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-21 16:02:33.111][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-21 16:02:33.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.117][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[2026-02-21 16:02:33.118][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-21 16:02:33.119][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-21 16:02:33.121][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-21 16:02:33.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.128][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-21 16:02:33.131][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-21 16:02:33.138][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-21 16:02:33.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.149][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-21 16:02:33.153][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-21 16:02:33.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.174][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-21 16:02:33.177][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-21 16:02:33.179][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-21 16:02:33.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.204][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-21 16:02:33.219][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-21 16:02:33.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.228][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-21 16:02:33.230][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-21 16:02:33.233][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-21 16:02:33.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.238][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[2026-02-21 16:02:33.241][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:02:33.243][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-21 16:02:33.245][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-21 16:02:33.247][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-21 16:02:33.249][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-21 16:02:33.252][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-21 16:02:33.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.261][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-21 16:02:33.263][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-21 16:02:33.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.269][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[2026-02-21 16:02:33.271][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-21 16:02:33.274][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-21 16:02:33.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.285][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-21 16:02:33.287][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-21 16:02:33.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.297][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-21 16:02:33.299][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-21 16:02:33.301][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-21 16:02:33.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.310][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:02:33.312][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-21 16:02:33.334][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-21 16:02:33.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.340][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[2026-02-21 16:02:33.342][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-21 16:02:33.344][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-21 16:02:33.347][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-21 16:02:33.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.356][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-21 16:02:33.360][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:33.362][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-21 16:02:33.365][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.367][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:33.369][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.372][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:33.374][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:33.377][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:33.379][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:02:33.382][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:33.384][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.387][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-21 16:02:33.389][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:33.391][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:33.393][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.396][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:33.396][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:33.396][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:33.396][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:02:33.396][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:02:33.398][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:33.401][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:33.403][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:33.406][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:33.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:33.410][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:33.412][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:33.414][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:33.416][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:33.418][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:33.420][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:33.423][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:33.426][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-21 16:02:33.430][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:33.433][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:02:33.435][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.437][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:33.439][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.441][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:33.444][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:33.446][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:33.448][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:02:33.451][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:33.453][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.455][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-21 16:02:33.457][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:33.459][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:33.461][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.463][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:33.463][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:33.463][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:33.463][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:02:33.463][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:02:33.464][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:33.471][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:33.473][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:33.475][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:33.477][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:33.478][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:33.479][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:33.480][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:33.482][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:33.483][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:33.484][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:33.486][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:33.488][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-21 16:02:33.491][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.492][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-21 16:02:33.493][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.495][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:33.497][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.499][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:33.500][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:33.502][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:33.503][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:02:33.504][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:33.505][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:33.507][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-21 16:02:33.508][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:33.509][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:33.510][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.512][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:33.513][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:33.514][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:33.515][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:33.517][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:33.518][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:33.519][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:33.520][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:33.521][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:33.522][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:33.524][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:33.525][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:33.526][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:33.527][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-21 16:02:33.530][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.531][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:02:33.532][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.533][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:33.535][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.536][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:33.537][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:33.538][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:33.540][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:02:33.541][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:33.542][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:33.543][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-21 16:02:33.545][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:33.546][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:33.547][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.549][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:33.550][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:33.551][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:33.552][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:33.553][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:33.555][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:33.556][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:33.557][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:33.558][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:33.559][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:33.560][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:33.562][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:33.563][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:33.564][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:33.566][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.594][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[2026-02-21 16:02:33.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.600][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[2026-02-21 16:02:33.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.617][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[2026-02-21 16:02:33.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.628][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[2026-02-21 16:02:33.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.633][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[2026-02-21 16:02:33.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.650][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[2026-02-21 16:02:33.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.660][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[2026-02-21 16:02:33.662][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-21 16:02:33.663][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-21 16:02:33.665][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-21 16:02:33.667][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-21 16:02:33.669][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-21 16:02:33.670][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-21 16:02:33.672][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-21 16:02:33.674][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-21 16:02:33.676][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-21 16:02:33.677][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-21 16:02:33.679][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-21 16:02:33.681][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-21 16:02:33.682][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-21 16:02:33.684][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-21 16:02:33.686][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-21 16:02:33.687][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-21 16:02:33.689][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-21 16:02:33.691][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-21 16:02:33.693][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-21 16:02:33.694][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-21 16:02:33.696][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-21 16:02:33.698][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-21 16:02:33.699][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-21 16:02:33.701][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-21 16:02:33.703][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-21 16:02:33.705][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-21 16:02:33.706][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-21 16:02:33.708][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-21 16:02:33.710][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-21 16:02:33.711][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-21 16:02:33.713][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-21 16:02:33.715][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-21 16:02:33.716][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-21 16:02:33.718][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-21 16:02:33.720][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-21 16:02:33.722][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-21 16:02:33.723][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-21 16:02:33.725][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-21 16:02:33.727][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-21 16:02:33.728][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-21 16:02:33.730][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-21 16:02:33.732][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-21 16:02:33.733][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-21 16:02:33.735][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-21 16:02:33.737][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-21 16:02:33.739][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-21 16:02:33.740][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-21 16:02:33.742][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-21 16:02:33.744][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-21 16:02:33.745][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-21 16:02:33.747][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-21 16:02:33.749][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-21 16:02:33.751][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-21 16:02:33.752][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-21 16:02:33.754][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-21 16:02:33.756][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-21 16:02:33.757][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-21 16:02:33.759][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-21 16:02:33.761][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-21 16:02:33.763][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-21 16:02:33.764][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-21 16:02:33.766][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-21 16:02:33.768][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-21 16:02:33.769][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-21 16:02:33.771][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-21 16:02:33.773][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-21 16:02:33.775][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-21 16:02:33.776][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-21 16:02:33.778][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-21 16:02:33.780][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-21 16:02:33.781][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-21 16:02:33.783][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-21 16:02:33.785][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-21 16:02:33.787][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-21 16:02:33.788][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-21 16:02:33.790][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-21 16:02:33.792][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-21 16:02:33.793][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-21 16:02:33.795][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-21 16:02:33.797][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-21 16:02:33.798][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-21 16:02:33.800][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-21 16:02:33.802][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-21 16:02:33.804][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-21 16:02:33.805][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:02:33.807][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:33.808][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.810][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.811][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[2026-02-21 16:02:33.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:33.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:33.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:33.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:33.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:33.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:33.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:33.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:33.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:33.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:33.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.855][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[2026-02-21 16:02:33.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:33.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:33.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:33.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:33.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:33.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:33.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:33.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:33.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:33.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:33.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:33.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:33.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:33.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:33.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:33.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:33.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:33.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:33.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:33.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:33.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:33.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:33.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:33.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:33.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:33.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:33.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:33.941][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[2026-02-21 16:02:33.943][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-02-21 16:02:33.945][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-02-21 16:02:33.947][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.949][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-02-21 16:02:33.950][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.951][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:33.953][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.954][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:33.955][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.956][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:33.957][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-02-21 16:02:33.959][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:33.960][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.961][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-02-21 16:02:33.963][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:33.964][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-02-21 16:02:33.964][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-02-21 16:02:33.965][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:33.966][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:33.968][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-21 16:02:33.969][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:33.970][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:33.971][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:33.972][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:33.973][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:33.975][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:33.976][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-21 16:02:33.976][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-02-21 16:02:33.977][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:33.978][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:33.979][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.981][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:33.982][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-02-21 16:02:33.985][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.986][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-02-21 16:02:33.987][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.989][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:33.990][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.991][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:33.992][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.994][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:33.995][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-21 16:02:33.996][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:33.997][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:33.999][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-02-21 16:02:34.000][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:34.001][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-02-21 16:02:34.001][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-02-21 16:02:34.001][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-02-21 16:02:34.001][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-02-21 16:02:34.001][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-02-21 16:02:34.001][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-02-21 16:02:34.003][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:34.009][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:34.010][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-21 16:02:34.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:34.013][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:34.014][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:34.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:34.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:34.017][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:34.019][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:34.019][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-21 16:02:34.020][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:34.021][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:34.022][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:34.023][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:34.025][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-02-21 16:02:34.027][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:34.029][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-02-21 16:02:34.030][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:34.031][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:34.033][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:34.034][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:34.035][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:34.036][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:34.038][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-21 16:02:34.039][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:34.040][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:34.041][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-02-21 16:02:34.043][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:34.044][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-21 16:02:34.044][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:34.044][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:34.044][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:34.044][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:34.044][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:34.044][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:34.044][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:34.044][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:34.044][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:34.044][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-02-21 16:02:34.044][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:34.044][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:34.044][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:34.046][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:34.047][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:34.047][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:34.047][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:34.048][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-21 16:02:34.049][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:34.051][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:34.052][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:34.053][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:34.054][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:34.055][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:34.057][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:34.057][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-21 16:02:34.057][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-21 16:02:34.058][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:34.059][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:34.061][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:34.062][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-21 16:02:34.063][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-02-21 16:02:34.066][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:34.067][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-02-21 16:02:34.068][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:34.070][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:34.071][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:34.072][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:34.073][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:34.075][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:34.076][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-21 16:02:34.077][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:34.078][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:34.080][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-02-21 16:02:34.081][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:34.082][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-02-21 16:02:34.082][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-21 16:02:34.083][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:34.085][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:34.086][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-21 16:02:34.087][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:34.088][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:34.089][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:34.091][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:34.092][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:34.093][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:34.094][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:34.094][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-21 16:02:34.094][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-21 16:02:34.095][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:34.096][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:34.098][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:34.099][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-21 16:02:34.101][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-02-21 16:02:34.102][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-21 16:02:34.104][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-21 16:02:34.106][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-02-21 16:02:34.108][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-21 16:02:34.110][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-02-21 16:02:34.118][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2026-02-21 16:02:34.123][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2026-02-21 16:02:34.128][biodb::testThat]
biodb.INFO [2026-02-21 16:02:34.129][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-21 16:02:34.131][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:34.132][biodb::testThat]
biodb.TRACE[2026-02-21 16:02:34.135][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2026-02-21 16:02:34.137][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2026-02-21 16:02:34.140][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2026-02-21 16:02:34.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-21 16:02:34.143][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:34.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:34.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:34.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:34.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:34.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-21 16:02:34.161][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.162][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.164][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.165][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.172][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.174][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.175][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.176][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.178][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.183][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.185][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.186][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.187][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.189][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.201][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.202][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.204][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.205][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.206][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.212][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:34.213][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:34.214][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.215][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.217][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:34.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:34.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.223][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:34.224][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:34.225][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.226][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.228][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:34.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:34.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.234][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-21 16:02:34.235][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:34.236][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.237][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.239][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-21 16:02:34.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:34.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.245][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:34.246][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:34.247][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.248][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.250][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:34.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:34.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.255][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:34.257][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:34.258][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.259][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:34.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:34.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.267][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:34.268][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:34.269][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.271][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.272][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:34.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:34.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.277][ef$get] Asked field names are: logp.
biodb.TRACE[2026-02-21 16:02:34.279][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-21 16:02:34.280][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.281][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.283][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-21 16:02:34.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-21 16:02:34.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.288][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-21 16:02:34.290][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:34.291][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.292][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-21 16:02:34.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:34.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.299][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:34.301][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:34.302][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.303][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.305][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:34.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:34.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.310][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:34.311][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:34.312][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.314][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.315][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:34.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:34.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.321][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2026-02-21 16:02:34.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.326][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.331][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.336][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2026-02-21 16:02:34.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.408][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.413][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.418][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2026-02-21 16:02:34.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:34.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.423][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:34.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:34.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.428][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:34.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:34.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.433][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2026-02-21 16:02:34.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:34.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.438][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:34.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:34.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.443][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:34.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:34.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.449][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2026-02-21 16:02:34.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.454][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.459][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.464][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:34.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:34.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.469][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:34.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:34.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.474][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:34.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:34.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.485][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:34.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:34.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-21 16:02:34.520][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2026-02-21 16:02:34.523][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-21 16:02:34.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:34.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.528][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-21 16:02:34.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:34.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.533][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:34.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:34.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.538][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:02:34.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:02:34.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.543][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:02:34.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:02:34.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.548][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-21 16:02:34.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-21 16:02:34.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.553][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-21 16:02:34.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-21 16:02:34.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.575][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:34.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:34.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.619][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:34.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:34.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.624][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:34.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:34.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.629][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:34.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:34.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.656][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.658][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.659][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.660][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:34.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:34.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.677][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-21 16:02:34.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:34.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:34.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:34.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:34.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:34.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.692][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-21 16:02:34.694][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:34.695][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.696][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.697][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-21 16:02:34.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:34.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-21 16:02:34.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:34.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:34.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:34.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:34.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:34.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.728][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-21 16:02:34.730][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:34.731][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.732][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-21 16:02:34.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:34.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.753][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:34.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:34.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.758][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:34.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:34.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.763][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:34.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:34.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.769][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:34.770][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:34.771][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.773][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.774][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:34.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:34.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.789][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-21 16:02:34.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-21 16:02:34.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.795][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-21 16:02:34.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-21 16:02:34.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.800][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-21 16:02:34.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-21 16:02:34.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.804][ef$get] Asked field names are: logp.
biodb.TRACE[2026-02-21 16:02:34.806][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-21 16:02:34.807][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.808][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.809][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-21 16:02:34.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-21 16:02:34.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.824][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:34.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:34.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.829][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:34.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:34.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.834][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:34.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:34.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.839][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:34.841][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:34.842][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.843][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.844][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:34.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:34.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.859][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:34.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:34.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.864][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:34.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:34.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.869][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:34.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:34.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.875][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:34.876][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:34.877][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.878][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.879][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:34.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:34.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.895][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.900][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.905][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.910][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.912][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.913][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.914][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.915][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:34.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.936][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.942][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.947][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.952][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.954][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.955][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.956][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.957][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:34.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.974][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.979][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.984][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.990][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.991][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.993][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.994][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:34.995][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:34.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:34.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.010][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.016][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.021][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.026][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.027][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.028][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.029][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.030][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.046][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.051][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.056][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.061][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.063][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.064][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.065][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.066][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.082][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:35.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:35.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.087][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:35.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:35.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.092][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:35.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:35.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.097][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:35.098][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:35.099][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.100][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:35.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:35.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:35.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:35.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.127][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:35.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:35.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.132][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:35.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:35.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.137][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:35.138][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:35.140][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.141][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.142][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:35.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:35.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.157][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:35.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:35.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.162][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:35.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:35.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.167][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:35.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:35.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.172][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:35.174][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:35.175][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.176][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.177][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:35.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:35.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.192][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.194][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.195][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.196][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.203][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:35.204][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:35.205][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.207][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.213][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:35.215][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:35.216][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.217][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.224][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:35.225][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:35.226][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.227][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.234][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.235][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.237][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.238][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.245][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.246][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.247][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.248][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.255][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:35.257][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:35.258][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.259][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.266][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:35.267][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:35.269][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.270][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.276][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:35.278][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:35.279][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.280][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.287][ef$get] Asked field names are: logp.
biodb.TRACE[2026-02-21 16:02:35.288][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-21 16:02:35.289][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.290][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.302][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:35.304][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:35.305][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.306][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.313][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:35.314][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:35.315][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.316][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.323][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:35.324][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:35.326][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.327][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.333][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:35.335][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:35.336][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.337][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.344][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:35.345][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:35.347][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.348][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.355][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2026-02-21 16:02:35.357][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2026-02-21 16:02:35.358][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2026-02-21 16:02:35.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-21 16:02:35.361][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:35.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:35.369][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:35.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:35.371][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:35.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-21 16:02:35.375][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.377][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.378][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.379][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.386][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:35.387][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:35.389][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.390][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.391][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:35.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:35.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.397][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:35.398][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:35.399][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.400][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.402][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:35.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:35.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.407][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:35.409][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:35.410][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.411][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.413][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:35.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:35.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.418][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.419][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.420][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.422][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.423][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.428][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.430][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.431][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.432][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.434][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.439][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-21 16:02:35.441][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:35.442][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.443][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.445][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-21 16:02:35.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:35.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.450][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:35.452][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:35.453][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.454][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.456][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:35.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:35.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.461][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:35.462][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:35.463][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.465][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.466][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:35.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:35.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.472][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:35.473][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:35.474][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.475][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:35.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:35.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.482][ef$get] Asked field names are: logp.
biodb.TRACE[2026-02-21 16:02:35.484][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-21 16:02:35.490][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.492][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.494][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-21 16:02:35.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-21 16:02:35.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.501][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-21 16:02:35.502][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:35.503][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.505][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-21 16:02:35.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:35.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.512][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:35.513][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:35.514][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.516][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.517][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:35.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:35.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.523][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:35.524][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:35.525][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.527][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.528][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:35.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:35.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.534][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2026-02-21 16:02:35.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:35.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.539][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:35.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:35.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.544][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:35.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:35.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.549][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2026-02-21 16:02:35.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:35.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.554][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:35.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:35.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.559][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:35.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:35.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.564][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2026-02-21 16:02:35.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.569][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.574][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:35.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.579][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2026-02-21 16:02:35.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.584][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.589][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:35.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.593][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2026-02-21 16:02:35.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:35.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.599][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:35.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:35.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.604][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:35.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:35.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.609][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:35.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:35.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.614][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:35.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:35.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.619][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:35.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:35.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.629][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:35.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:35.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-21 16:02:35.667][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2026-02-21 16:02:35.675][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-21 16:02:35.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:35.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.682][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-21 16:02:35.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:35.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.687][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:35.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:35.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.693][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:02:35.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:02:35.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.698][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:02:35.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:02:35.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.704][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-21 16:02:35.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-21 16:02:35.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.709][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-21 16:02:35.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-21 16:02:35.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.726][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:35.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:35.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.769][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:35.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:35.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.774][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:35.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:35.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.779][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:35.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:35.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.807][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.808][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.810][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.811][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:35.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:35.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:35.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:35.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:35.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:35.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:35.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:35.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.845][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:35.847][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:35.848][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.849][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:35.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:35.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:35.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:35.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:35.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:35.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:35.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:35.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.889][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:35.890][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:35.891][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.892][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.894][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:35.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:35.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.910][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:35.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:35.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.916][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:35.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:35.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.922][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:35.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:35.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.927][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:35.928][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:35.930][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.931][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.932][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:35.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:35.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.949][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-21 16:02:35.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-21 16:02:35.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.954][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-21 16:02:35.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-21 16:02:35.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.959][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-21 16:02:35.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-21 16:02:35.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.964][ef$get] Asked field names are: logp.
biodb.TRACE[2026-02-21 16:02:35.966][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-21 16:02:35.967][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.968][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.969][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-21 16:02:35.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-21 16:02:35.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.985][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:35.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:35.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.990][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:35.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:35.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:35.995][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:35.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:35.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:35.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.000][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:36.002][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:36.003][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.004][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.005][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:36.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:36.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.021][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:36.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:36.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.026][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:36.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:36.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.031][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:36.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:36.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.036][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:36.038][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:36.039][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.040][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.041][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:36.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:36.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:36.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:36.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.067][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:36.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:36.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.072][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:36.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:36.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.077][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:36.078][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:36.079][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.081][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.082][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:36.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:36.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.097][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:36.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:36.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:36.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:36.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.107][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:36.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:36.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.112][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:36.113][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:36.115][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.116][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.117][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:36.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:36.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.132][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:36.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:36.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.138][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:36.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:36.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.143][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:36.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:36.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.148][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:36.149][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:36.150][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.152][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.153][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:36.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:36.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.168][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:36.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:36.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.174][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:36.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:36.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.179][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:36.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:36.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.184][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:36.185][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:36.187][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.188][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.189][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:36.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:36.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.205][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:36.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:36.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.211][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:36.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:36.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.216][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:36.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:36.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.221][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:36.223][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:36.228][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.230][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.231][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:36.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:36.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.248][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:36.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:36.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.253][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:36.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:36.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.258][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:36.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:36.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.263][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:36.265][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:36.266][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.267][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.268][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:36.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:36.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.284][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:36.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:36.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.289][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:36.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:36.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.294][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:36.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:36.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.299][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:36.300][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:36.302][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.303][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.304][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:36.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:36.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.319][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:36.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:36.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.325][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:36.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:36.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.330][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:36.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:36.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.335][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:36.336][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:36.337][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.339][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.340][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:36.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:36.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.355][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:36.357][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:36.358][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.359][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.366][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:36.367][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-21 16:02:36.368][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.369][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.376][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:36.377][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-21 16:02:36.379][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.380][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.386][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:36.388][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-21 16:02:36.389][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.390][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.396][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:36.398][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:36.399][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.400][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.407][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:36.408][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:36.414][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.416][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.424][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:36.425][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:36.426][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.428][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.434][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:36.436][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:36.437][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.438][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.445][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:36.446][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:36.447][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.449][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.455][ef$get] Asked field names are: logp.
biodb.TRACE[2026-02-21 16:02:36.457][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-21 16:02:36.458][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.459][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.466][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:36.467][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:36.468][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.469][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.476][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:36.477][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:36.478][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.480][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.486][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:36.488][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:36.489][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.490][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.496][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:36.498][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-21 16:02:36.499][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.500][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:36.506][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:36.508][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-21 16:02:36.509][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.510][ef$get] fields variable is a list.
biodb.INFO [2026-02-21 16:02:36.521][biodb::testThat]
biodb.INFO [2026-02-21 16:02:36.522][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-21 16:02:36.523][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:36.524][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:36.527][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-02-21 16:02:36.531][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-02-21 16:02:36.533][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-21 16:02:36.535][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:36.536][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:36.537][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:36.539][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-21 16:02:36.540][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-21 16:02:36.601][biodb::testThat]
biodb.INFO [2026-02-21 16:02:36.603][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-21 16:02:36.604][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:36.605][biodb::testThat]
biodb.TRACE[2026-02-21 16:02:36.609][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:36.610][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:36.612][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:36.613][ef$get] fields variable is a list.
biodb.DEBUG[2026-02-21 16:02:36.614][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2026-02-21 16:02:36.626][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-02-21 16:02:36.627][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-02-21 16:02:36.629][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-21 16:02:36.630][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:36.632][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:36.633][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:36.634][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-21 16:02:36.636][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-21 16:02:36.694][biodb::testThat]
biodb.INFO [2026-02-21 16:02:36.695][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-21 16:02:36.696][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:36.697][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:36.707][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-02-21 16:02:36.709][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-02-21 16:02:36.711][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-21 16:02:36.712][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:36.713][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:36.715][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:36.716][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-21 16:02:36.717][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-21 16:02:36.780][biodb::testThat]
biodb.INFO [2026-02-21 16:02:36.782][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-21 16:02:36.783][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:36.784][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:36.789][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-02-21 16:02:36.791][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-02-21 16:02:36.792][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-21 16:02:36.794][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:36.795][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:36.796][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:36.798][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-21 16:02:36.799][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-21 16:02:36.857][biodb::testThat]
biodb.INFO [2026-02-21 16:02:36.858][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-21 16:02:36.860][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:36.861][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-21 16:02:36.926][biodb::testThat]
biodb.INFO [2026-02-21 16:02:36.927][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-21 16:02:36.928][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:36.929][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-21 16:02:36.988][biodb::testThat]
biodb.INFO [2026-02-21 16:02:36.990][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-21 16:02:36.991][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:36.992][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-21 16:02:37.052][biodb::testThat]
biodb.INFO [2026-02-21 16:02:37.053][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-21 16:02:37.054][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:37.056][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2026-02-21 16:02:37.128][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:37.129][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:37.131][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:37.132][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:37.133][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:37.134][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:37.136][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:37.137][ef$get] fields variable is a list.
biodb.INFO [2026-02-21 16:02:37.139][biodb::testThat]
biodb.INFO [2026-02-21 16:02:37.140][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2026-02-21 16:02:37.141][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:37.143][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:37.152][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-02-21 16:02:37.153][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-02-21 16:02:37.155][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-21 16:02:37.157][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:37.158][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:37.159][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:37.161][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-21 16:02:37.162][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-21 16:02:37.220][biodb::testThat]
biodb.INFO [2026-02-21 16:02:37.221][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2026-02-21 16:02:37.223][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:37.224][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:37.227][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-02-21 16:02:37.229][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-02-21 16:02:37.231][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-21 16:02:37.236][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:37.238][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:37.239][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:37.240][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-21 16:02:37.242][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-21 16:02:37.300][biodb::testThat]
biodb.INFO [2026-02-21 16:02:37.301][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2026-02-21 16:02:37.302][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:37.303][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:37.307][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-02-21 16:02:37.308][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-02-21 16:02:37.310][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-21 16:02:37.311][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:37.313][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:37.314][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:37.315][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-21 16:02:37.316][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-21 16:02:37.374][biodb::testThat]
biodb.INFO [2026-02-21 16:02:37.375][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2026-02-21 16:02:37.377][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:37.378][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:37.382][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-02-21 16:02:37.383][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-02-21 16:02:37.385][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-21 16:02:37.386][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:37.388][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:37.393][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:37.395][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-21 16:02:37.396][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2026-02-21 16:02:37.453][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:37.455][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:37.456][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:37.457][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:37.459][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:37.460][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:37.461][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:37.462][ef$get] fields variable is a list.
biodb.INFO [2026-02-21 16:02:37.464][biodb::testThat]
biodb.INFO [2026-02-21 16:02:37.466][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2026-02-21 16:02:37.467][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:37.468][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:37.472][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-02-21 16:02:37.473][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-02-21 16:02:37.475][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-21 16:02:37.476][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:37.478][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:37.479][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:37.480][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-21 16:02:37.482][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-21 16:02:37.539][biodb::testThat]
biodb.INFO [2026-02-21 16:02:37.541][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2026-02-21 16:02:37.542][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:37.543][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:37.551][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-02-21 16:02:37.553][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-02-21 16:02:37.555][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-21 16:02:37.556][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:37.557][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:37.559][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:37.560][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-21 16:02:37.561][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-21 16:02:37.617][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-21 16:02:37.619][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2026-02-21 16:02:37.620][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-21 16:02:37.621][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:37.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:37.623][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:37.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:37.626][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-02-21 16:02:37.632][biodb::testContext]
biodb.INFO [2026-02-21 16:02:37.633][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:02:37.634][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2026-02-21 16:02:37.635][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:02:37.636][biodb::testContext]
biodb.INFO [2026-02-21 16:02:37.639][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:02:37.641][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-21 16:02:37.645][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:37.646][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-21 16:02:37.648][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-21 16:02:37.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.652][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-21 16:02:37.654][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-21 16:02:37.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.658][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-21 16:02:37.659][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-21 16:02:37.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.664][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-21 16:02:37.665][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-21 16:02:37.666][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-21 16:02:37.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.671][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-21 16:02:37.672][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-21 16:02:37.673][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-21 16:02:37.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.678][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-21 16:02:37.679][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-21 16:02:37.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.683][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-21 16:02:37.685][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-21 16:02:37.686][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-21 16:02:37.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.690][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-21 16:02:37.691][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-21 16:02:37.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.696][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-21 16:02:37.697][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-21 16:02:37.699][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-21 16:02:37.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.703][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:02:37.704][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-21 16:02:37.706][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-21 16:02:37.711][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-21 16:02:37.713][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-21 16:02:37.714][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-21 16:02:37.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.719][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-21 16:02:37.720][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-21 16:02:37.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.724][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-21 16:02:37.726][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-21 16:02:37.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.730][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-21 16:02:37.731][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-21 16:02:37.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.736][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-21 16:02:37.737][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-21 16:02:37.738][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-21 16:02:37.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.743][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:02:37.744][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-21 16:02:37.754][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-21 16:02:37.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.759][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-21 16:02:37.760][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-21 16:02:37.761][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-21 16:02:37.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.766][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-21 16:02:37.768][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:37.769][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-21 16:02:37.770][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:37.772][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:37.773][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:37.774][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:37.775][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:37.777][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:37.778][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:02:37.779][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:37.781][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:37.782][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-21 16:02:37.783][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:37.784][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:37.786][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:37.787][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:37.787][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:37.787][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:37.787][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:02:37.787][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:02:37.788][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:37.789][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:37.790][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:37.792][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:37.793][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:37.794][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:37.795][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:37.796][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:37.798][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:37.799][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:37.800][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:37.801][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:37.803][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-21 16:02:37.805][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:37.806][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:02:37.807][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:37.809][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:37.810][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:37.811][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:37.812][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:37.814][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:37.815][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:02:37.816][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:37.818][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:37.819][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-21 16:02:37.820][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:37.821][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:37.823][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:37.824][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:37.824][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:37.824][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:37.824][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:02:37.824][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:02:37.825][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:37.827][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:37.828][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:37.829][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:37.830][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:37.831][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:37.833][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:37.834][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:37.835][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:37.836][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:37.838][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:37.839][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:37.840][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-21 16:02:37.843][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:37.844][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-21 16:02:37.845][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:37.846][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:37.848][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:37.849][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:37.850][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:37.851][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:37.853][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:02:37.854][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:37.855][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:37.857][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-21 16:02:37.858][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:37.859][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:37.861][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:37.862][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:37.863][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:37.864][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:37.865][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:37.867][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:37.868][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:37.869][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:37.870][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:37.872][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:37.873][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:37.874][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:37.875][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:37.876][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:37.878][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-21 16:02:37.880][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:37.887][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:02:37.888][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:37.890][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:37.891][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:37.892][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:37.894][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:37.895][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:37.896][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:02:37.897][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:37.899][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:37.900][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-21 16:02:37.901][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:37.902][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:37.904][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:37.905][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:37.906][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:37.907][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:37.909][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:37.910][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:37.911][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:37.912][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:37.913][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:37.915][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:37.916][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:37.917][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:37.918][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:37.920][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:37.921][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:37.922][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.924][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[2026-02-21 16:02:37.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:37.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:37.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:37.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:37.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:37.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:37.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.941][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[2026-02-21 16:02:37.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:37.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:37.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:37.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:37.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:37.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:37.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:37.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:37.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:37.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:37.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:37.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:37.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:37.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:37.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:37.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:37.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:37.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:37.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:37.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:37.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:37.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:37.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:37.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:38.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:38.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:38.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:38.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:38.015][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-21 16:02:38.017][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-21 16:02:38.019][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-21 16:02:38.020][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-21 16:02:38.022][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-21 16:02:38.024][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-21 16:02:38.025][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-21 16:02:38.027][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-21 16:02:38.029][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-21 16:02:38.030][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-21 16:02:38.032][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-21 16:02:38.034][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-21 16:02:38.036][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-21 16:02:38.037][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-21 16:02:38.039][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-21 16:02:38.041][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-21 16:02:38.042][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-21 16:02:38.044][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-21 16:02:38.046][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-21 16:02:38.055][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-21 16:02:38.057][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-21 16:02:38.058][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-21 16:02:38.060][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-21 16:02:38.062][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-21 16:02:38.064][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-21 16:02:38.066][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-21 16:02:38.067][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-21 16:02:38.069][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-21 16:02:38.071][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-21 16:02:38.073][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-21 16:02:38.074][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-21 16:02:38.076][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-21 16:02:38.078][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-21 16:02:38.079][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-21 16:02:38.081][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-21 16:02:38.083][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-21 16:02:38.085][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-21 16:02:38.086][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-21 16:02:38.088][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-21 16:02:38.090][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-21 16:02:38.091][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-21 16:02:38.093][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-21 16:02:38.095][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-21 16:02:38.097][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-21 16:02:38.098][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-21 16:02:38.100][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-21 16:02:38.102][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-21 16:02:38.103][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-21 16:02:38.105][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-21 16:02:38.107][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-21 16:02:38.109][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-21 16:02:38.110][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-21 16:02:38.112][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-21 16:02:38.114][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-21 16:02:38.115][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-21 16:02:38.117][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-21 16:02:38.119][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-21 16:02:38.121][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-21 16:02:38.122][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-21 16:02:38.124][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-21 16:02:38.126][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-21 16:02:38.128][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-21 16:02:38.129][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-21 16:02:38.131][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-21 16:02:38.133][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-21 16:02:38.134][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-21 16:02:38.136][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-21 16:02:38.138][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-21 16:02:38.140][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-21 16:02:38.141][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-21 16:02:38.143][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-21 16:02:38.145][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-21 16:02:38.146][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-21 16:02:38.148][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-21 16:02:38.150][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-21 16:02:38.152][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-21 16:02:38.153][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-21 16:02:38.155][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-21 16:02:38.157][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-21 16:02:38.159][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-21 16:02:38.160][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-21 16:02:38.162][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-21 16:02:38.164][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-21 16:02:38.165][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-21 16:02:38.167][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:02:38.169][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:38.170][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.172][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:38.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:38.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:38.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:38.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:38.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:38.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:38.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:38.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:38.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:38.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:38.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:38.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.197][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[2026-02-21 16:02:38.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:38.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:38.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:38.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:38.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:38.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:38.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:38.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:38.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:38.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:38.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:38.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.227][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[2026-02-21 16:02:38.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:38.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:38.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:38.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.235][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[2026-02-21 16:02:38.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:38.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:38.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:38.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:38.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:38.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:38.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:38.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:38.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:38.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:38.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:38.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:38.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:38.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:38.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:38.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:38.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:38.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:38.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:38.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.275][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[2026-02-21 16:02:38.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:38.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:38.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:38.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:38.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:38.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:38.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:38.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.291][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[2026-02-21 16:02:38.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:38.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:38.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:38.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:38.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:38.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:38.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:38.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.307][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[2026-02-21 16:02:38.309][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-02-21 16:02:38.323][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-02-21 16:02:38.326][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.327][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-02-21 16:02:38.328][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.330][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:38.331][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.333][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:38.334][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.335][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:38.336][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-02-21 16:02:38.338][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:38.339][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.340][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-02-21 16:02:38.342][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:38.343][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-02-21 16:02:38.343][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-02-21 16:02:38.344][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:38.346][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:38.347][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-21 16:02:38.348][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:38.349][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:38.350][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:38.352][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:38.353][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:38.354][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:38.355][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-21 16:02:38.355][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-02-21 16:02:38.357][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:38.358][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:38.359][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.360][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:38.362][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-02-21 16:02:38.364][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.366][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-02-21 16:02:38.367][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.368][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:38.369][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.371][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:38.372][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.373][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:38.374][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-21 16:02:38.376][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:38.377][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.378][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-02-21 16:02:38.380][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:38.381][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-02-21 16:02:38.381][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-02-21 16:02:38.381][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-02-21 16:02:38.381][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-02-21 16:02:38.381][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-02-21 16:02:38.381][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-02-21 16:02:38.382][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:38.384][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:38.385][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-21 16:02:38.386][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:38.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:38.388][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:38.395][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:38.396][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:38.397][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:38.399][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:38.399][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-21 16:02:38.400][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:38.401][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:38.403][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.404][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:38.405][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-02-21 16:02:38.408][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:38.409][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-02-21 16:02:38.410][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.412][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:38.413][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.414][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:38.416][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.417][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:38.418][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-21 16:02:38.419][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:38.421][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.422][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-02-21 16:02:38.423][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:38.425][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-21 16:02:38.425][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:38.425][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:38.425][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:38.425][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:38.425][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:38.425][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:38.425][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:38.425][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:38.425][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:38.425][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-02-21 16:02:38.425][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:38.425][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:38.425][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-21 16:02:38.426][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:38.427][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:38.427][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:38.427][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:38.429][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-21 16:02:38.430][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:38.431][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:38.432][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:38.434][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:38.435][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:38.436][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:38.437][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:38.437][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-21 16:02:38.437][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-21 16:02:38.439][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:38.440][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:38.441][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.442][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-21 16:02:38.444][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-02-21 16:02:38.446][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.447][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-02-21 16:02:38.449][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.450][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:38.451][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.452][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:38.454][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.455][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:38.456][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-21 16:02:38.458][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:38.459][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.460][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-02-21 16:02:38.461][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:38.463][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-02-21 16:02:38.463][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-21 16:02:38.464][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:38.465][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:38.467][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-21 16:02:38.468][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:38.469][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:38.470][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:38.472][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:38.473][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:38.474][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:38.476][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:38.476][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-21 16:02:38.476][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-21 16:02:38.477][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:38.478][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:38.479][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:38.481][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-21 16:02:38.482][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-02-21 16:02:38.485][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-21 16:02:38.487][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-21 16:02:38.489][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-02-21 16:02:38.491][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-21 16:02:38.493][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-02-21 16:02:38.499][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2026-02-21 16:02:38.505][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2026-02-21 16:02:38.510][biodb::testThat]
biodb.INFO [2026-02-21 16:02:38.511][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-21 16:02:38.513][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:38.514][biodb::testThat]
biodb.TRACE[2026-02-21 16:02:38.517][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2026-02-21 16:02:38.519][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2026-02-21 16:02:38.523][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2026-02-21 16:02:38.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-21 16:02:38.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:38.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:38.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:38.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:38.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:38.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-21 16:02:38.541][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.543][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.544][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.545][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.552][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:38.554][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:38.555][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.556][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.558][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:38.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:38.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.563][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-21 16:02:38.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-21 16:02:38.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.569][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-21 16:02:38.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-21 16:02:38.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.587][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-21 16:02:38.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-21 16:02:38.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-21 16:02:38.625][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2026-02-21 16:02:38.628][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-21 16:02:38.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:38.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.633][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-21 16:02:38.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-21 16:02:38.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.638][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:38.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-21 16:02:38.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.643][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:02:38.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:02:38.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.649][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:02:38.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:02:38.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.654][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-21 16:02:38.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-21 16:02:38.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.659][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-21 16:02:38.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-21 16:02:38.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.676][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-21 16:02:38.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-21 16:02:38.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.721][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-21 16:02:38.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-21 16:02:38.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.728][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-21 16:02:38.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-21 16:02:38.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.734][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-21 16:02:38.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-21 16:02:38.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.773][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.775][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.776][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.777][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.794][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:38.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:38.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.800][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:38.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:38.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.805][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:38.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:38.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.810][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:38.811][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:38.812][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.813][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.815][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:38.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:38.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.830][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:38.832][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:38.833][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.834][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:38.841][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:38.842][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:38.844][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:38.845][ef$get] fields variable is a list.
biodb.INFO [2026-02-21 16:02:38.855][biodb::testThat]
biodb.INFO [2026-02-21 16:02:38.857][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-21 16:02:38.858][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:38.859][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:38.862][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2026-02-21 16:02:38.866][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2026-02-21 16:02:38.868][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-21 16:02:38.870][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:38.871][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:38.872][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:38.874][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-21 16:02:38.875][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-02-21 16:02:38.939][biodb::testThat]
biodb.INFO [2026-02-21 16:02:38.940][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-21 16:02:38.942][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:38.943][biodb::testThat]
biodb.INFO [2026-02-21 16:02:38.952][biodb::testThat]
biodb.INFO [2026-02-21 16:02:38.953][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-21 16:02:38.954][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:38.955][biodb::testThat]
biodb.WARN [2026-02-21 16:02:38.959][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-02-21 16:02:38.963][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-02-21 16:02:38.974][biodb::testThat]
biodb.INFO [2026-02-21 16:02:38.976][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-21 16:02:38.977][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:38.978][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:38.983][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2026-02-21 16:02:38.985][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2026-02-21 16:02:38.987][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-21 16:02:38.988][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2026-02-21 16:02:38.989][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:38.991][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-21 16:02:38.992][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-21 16:02:38.993][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-02-21 16:02:39.051][biodb::testThat]
biodb.INFO [2026-02-21 16:02:39.052][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-21 16:02:39.054][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:39.055][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-02-21 16:02:39.120][biodb::testThat]
biodb.INFO [2026-02-21 16:02:39.121][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-21 16:02:39.123][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:39.124][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-02-21 16:02:39.183][biodb::testThat]
biodb.INFO [2026-02-21 16:02:39.184][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-21 16:02:39.185][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:39.187][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-02-21 16:02:39.249][biodb::testThat]
biodb.INFO [2026-02-21 16:02:39.250][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-21 16:02:39.252][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:39.253][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-02-21 16:02:39.320][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-21 16:02:39.321][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2026-02-21 16:02:39.322][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-21 16:02:39.324][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:39.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:39.326][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:39.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:39.328][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:39.329][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".
[ 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)