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"	4897
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4691
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: 2026-04-04 16:01:13 -0400 (Sat, 04 Apr 2026)

EndedAt: 2026-04-04 16:02:24 -0400 (Sat, 04 Apr 2026)

EllapsedTime: 70.7 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 [2026-04-04 16:02:12.285][biodb::testContext]
biodb.INFO [2026-04-04 16:02:12.289][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:02:12.290][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2026-04-04 16:02:12.291][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:02:12.292][biodb::testContext]
biodb.INFO [2026-04-04 16:02:12.299][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:02:12.302][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-04-04 16:02:12.309][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:12.311][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-04-04 16:02:12.312][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-04-04 16:02:12.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.317][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-04-04 16:02:12.341][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-04-04 16:02:12.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.346][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-04-04 16:02:12.347][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-04-04 16:02:12.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.352][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-04-04 16:02:12.353][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-04-04 16:02:12.354][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-04-04 16:02:12.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.359][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-04-04 16:02:12.360][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-04-04 16:02:12.362][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-04-04 16:02:12.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.366][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-04-04 16:02:12.368][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-04-04 16:02:12.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.372][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-04-04 16:02:12.373][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-04-04 16:02:12.375][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-04-04 16:02:12.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.379][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-04-04 16:02:12.381][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-04-04 16:02:12.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.385][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-04-04 16:02:12.386][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-04-04 16:02:12.388][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-04-04 16:02:12.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.392][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:02:12.394][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-04-04 16:02:12.395][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-04-04 16:02:12.396][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-04-04 16:02:12.397][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-04-04 16:02:12.399][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-04-04 16:02:12.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.403][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-04-04 16:02:12.405][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-04-04 16:02:12.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.409][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-04-04 16:02:12.411][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-04-04 16:02:12.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.416][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-04-04 16:02:12.417][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-04-04 16:02:12.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.422][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-04-04 16:02:12.423][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-04-04 16:02:12.424][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-04-04 16:02:12.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.429][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:02:12.430][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-04-04 16:02:12.441][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-04-04 16:02:12.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.446][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-04-04 16:02:12.447][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-04-04 16:02:12.448][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-04-04 16:02:12.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.456][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-04-04 16:02:12.500][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.528][self$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[2026-04-04 16:02:12.529][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.531][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:12.532][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.533][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.534][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.536][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.537][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:02:12.538][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:12.540][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.541][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-04-04 16:02:12.542][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:12.543][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.545][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.546][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:12.546][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:12.546][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:12.546][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:02:12.546][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:02:12.547][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:12.549][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:12.550][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:12.551][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:12.552][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:12.553][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:12.554][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.556][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.557][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:12.558][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:12.559][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.561][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.562][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-04-04 16:02:12.564][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.566][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:02:12.567][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.568][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:12.570][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.571][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.572][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.573][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.575][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:02:12.576][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:12.577][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.578][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-04-04 16:02:12.580][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:12.581][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.582][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.583][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:12.583][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:12.583][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:12.583][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:02:12.583][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:02:12.585][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:12.586][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:12.587][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:12.588][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:12.590][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:12.591][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:12.592][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.593][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.595][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:12.596][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:12.597][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.598][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.600][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-04-04 16:02:12.602][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.603][self$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[2026-04-04 16:02:12.604][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.605][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:12.607][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.608][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.609][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.611][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.612][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:02:12.613][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:12.614][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.616][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-04-04 16:02:12.617][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:12.618][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.619][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.621][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.622][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:12.623][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:12.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:12.626][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:12.627][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:12.628][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:12.629][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.630][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.632][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:12.633][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:12.634][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.635][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.637][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-04-04 16:02:12.639][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.640][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:02:12.641][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.643][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:12.644][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.645][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.646][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.648][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.649][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:02:12.650][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:12.651][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.653][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-04-04 16:02:12.654][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:12.655][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.656][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.658][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.659][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:12.660][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:12.661][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:12.662][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:12.664][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:12.665][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:12.666][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.667][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.668][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:12.669][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:12.671][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.672][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.676][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:12.677][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.723][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[2026-04-04 16:02:12.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.729][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[2026-04-04 16:02:12.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.735][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[2026-04-04 16:02:12.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.740][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[2026-04-04 16:02:12.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.757][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[2026-04-04 16:02:12.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.769][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-04-04 16:02:12.777][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-04-04 16:02:12.779][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-04-04 16:02:12.781][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-04-04 16:02:12.782][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-04-04 16:02:12.784][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-04-04 16:02:12.786][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-04-04 16:02:12.787][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-04-04 16:02:12.789][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-04-04 16:02:12.791][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-04-04 16:02:12.792][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-04-04 16:02:12.794][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-04-04 16:02:12.796][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-04-04 16:02:12.797][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-04-04 16:02:12.799][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-04-04 16:02:12.801][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-04-04 16:02:12.802][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-04-04 16:02:12.804][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-04-04 16:02:12.806][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-04-04 16:02:12.807][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-04-04 16:02:12.809][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-04-04 16:02:12.811][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-04-04 16:02:12.812][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-04-04 16:02:12.814][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-04-04 16:02:12.816][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-04-04 16:02:12.817][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-04-04 16:02:12.819][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-04-04 16:02:12.821][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-04-04 16:02:12.822][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-04-04 16:02:12.824][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-04-04 16:02:12.826][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-04-04 16:02:12.827][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-04-04 16:02:12.829][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-04-04 16:02:12.831][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-04-04 16:02:12.832][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-04-04 16:02:12.834][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-04-04 16:02:12.836][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-04-04 16:02:12.837][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-04-04 16:02:12.839][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-04-04 16:02:12.841][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-04-04 16:02:12.843][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-04-04 16:02:12.844][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-04-04 16:02:12.846][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-04-04 16:02:12.848][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-04-04 16:02:12.849][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-04-04 16:02:12.851][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-04-04 16:02:12.853][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-04-04 16:02:12.854][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-04-04 16:02:12.856][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-04-04 16:02:12.858][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-04-04 16:02:12.860][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-04-04 16:02:12.861][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-04-04 16:02:12.863][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-04-04 16:02:12.865][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-04-04 16:02:12.867][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-04-04 16:02:12.868][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-04-04 16:02:12.870][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-04-04 16:02:12.872][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-04-04 16:02:12.874][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-04-04 16:02:12.875][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-04-04 16:02:12.877][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-04-04 16:02:12.879][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-04-04 16:02:12.880][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-04-04 16:02:12.882][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-04-04 16:02:12.884][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-04-04 16:02:12.885][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-04-04 16:02:12.887][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-04-04 16:02:12.889][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-04-04 16:02:12.891][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-04-04 16:02:12.892][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-04-04 16:02:12.894][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-04-04 16:02:12.896][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-04-04 16:02:12.897][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-04-04 16:02:12.899][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-04-04 16:02:12.901][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-04-04 16:02:12.903][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-04-04 16:02:12.904][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-04-04 16:02:12.906][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-04-04 16:02:12.908][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-04-04 16:02:12.910][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-04-04 16:02:12.911][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-04-04 16:02:12.913][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-04-04 16:02:12.915][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-04-04 16:02:12.922][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-04-04 16:02:12.924][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:02:12.928][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:12.929][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.931][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.969][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[2026-04-04 16:02:12.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:13.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:13.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:13.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:13.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:13.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:13.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:13.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:13.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:13.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:13.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:13.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:13.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:13.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:13.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:13.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:13.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:13.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:13.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:13.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:13.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:13.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:13.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:13.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:13.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:13.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:13.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:13.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:13.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:13.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:13.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:13.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:13.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:13.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:13.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:13.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:13.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:13.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:13.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:13.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:13.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:13.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:13.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:13.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:13.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:13.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:13.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:13.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:13.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:13.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:13.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:13.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:13.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:13.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:13.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:13.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:13.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:13.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:13.071][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[2026-04-04 16:02:13.074][bdb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-04-04 16:02:13.087][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-04-04 16:02:13.089][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.091][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-04-04 16:02:13.092][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.093][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:13.094][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.096][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:13.097][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.098][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:13.099][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-04-04 16:02:13.101][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:13.102][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.103][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-04-04 16:02:13.105][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:13.106][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-04-04 16:02:13.106][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-04-04 16:02:13.107][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:13.108][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:13.110][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-04-04 16:02:13.111][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:13.112][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:13.113][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:13.115][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:13.116][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:13.117][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:13.118][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-04-04 16:02:13.118][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-04-04 16:02:13.119][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:13.121][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:13.122][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.123][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:13.125][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-04-04 16:02:13.127][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.128][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-04-04 16:02:13.130][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.131][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:13.132][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.133][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:13.135][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.136][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:13.137][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-04-04 16:02:13.139][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:13.140][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.141][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-04-04 16:02:13.143][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:13.144][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-04-04 16:02:13.144][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-04-04 16:02:13.144][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-04-04 16:02:13.144][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-04-04 16:02:13.144][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-04-04 16:02:13.144][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-04-04 16:02:13.145][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:13.147][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:13.148][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-04-04 16:02:13.149][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:13.150][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:13.152][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:13.153][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:13.154][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:13.155][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:13.157][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:13.157][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-04-04 16:02:13.158][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:13.159][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:13.160][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.162][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:13.163][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-04-04 16:02:13.166][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:13.167][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-04-04 16:02:13.169][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.170][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:13.171][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.172][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:13.174][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.175][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:13.176][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-04-04 16:02:13.177][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:13.179][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.180][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-04-04 16:02:13.181][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-04-04 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-04-04 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:13.184][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:13.186][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:13.186][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:13.186][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:13.187][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-04-04 16:02:13.188][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:13.189][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:13.191][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:13.192][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:13.193][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:13.194][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:13.195][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:13.195][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-04-04 16:02:13.195][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-04-04 16:02:13.197][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:13.198][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:13.199][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.200][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-04-04 16:02:13.202][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-04-04 16:02:13.204][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.206][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-04-04 16:02:13.207][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.208][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:13.210][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.211][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:13.212][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.213][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:13.215][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-04-04 16:02:13.216][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:13.217][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.218][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-04-04 16:02:13.220][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:13.221][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-04-04 16:02:13.221][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-04-04 16:02:13.222][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:13.224][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:13.225][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-04-04 16:02:13.226][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:13.227][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:13.229][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:13.230][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:13.231][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:13.232][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:13.233][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:13.233][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-04-04 16:02:13.233][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-04-04 16:02:13.235][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:13.236][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:13.237][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.238][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-04-04 16:02:13.246][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-04-04 16:02:13.248][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-04-04 16:02:13.250][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-04-04 16:02:13.252][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-04-04 16:02:13.254][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-04-04 16:02:13.255][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-04-04 16:02:13.276][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2026-04-04 16:02:13.291][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2026-04-04 16:02:13.306][biodb::testThat]
biodb.INFO [2026-04-04 16:02:13.308][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-04-04 16:02:13.309][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:13.310][biodb::testThat]
biodb.TRACE[2026-04-04 16:02:13.314][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2026-04-04 16:02:13.316][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2026-04-04 16:02:13.320][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2026-04-04 16:02:13.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-04-04 16:02:13.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:13.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:13.344][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:13.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:13.347][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:13.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-04-04 16:02:13.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.389][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-04-04 16:02:13.406][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:13.407][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.409][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.445][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-04-04 16:02:13.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:13.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.450][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.455][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.466][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-04-04 16:02:13.559][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2026-04-04 16:02:13.562][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-04-04 16:02:13.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:13.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.567][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-04-04 16:02:13.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:13.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.605][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:02:13.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:02:13.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.610][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:02:13.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:02:13.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.615][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-04-04 16:02:13.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-04-04 16:02:13.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.620][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-04-04 16:02:13.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-04-04 16:02:13.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.648][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.694][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.699][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.704][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.734][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.735][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.736][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.738][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.755][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-04-04 16:02:13.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:13.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.761][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-04-04 16:02:13.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:13.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.770][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-04-04 16:02:13.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:13.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.775][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-04-04 16:02:13.777][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:13.778][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.779][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.780][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-04-04 16:02:13.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:13.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.796][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2026-04-04 16:02:13.797][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:13.799][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.800][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.806][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.808][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.809][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.810][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.833][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2026-04-04 16:02:13.881][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2026-04-04 16:02:13.882][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2026-04-04 16:02:13.884][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-04-04 16:02:13.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:13.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:13.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:13.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:13.895][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:13.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-04-04 16:02:13.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.939][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-04-04 16:02:13.941][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:13.942][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.943][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.945][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-04-04 16:02:13.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:13.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.950][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.955][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.965][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:13.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-04-04 16:02:14.036][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2026-04-04 16:02:14.063][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-04-04 16:02:14.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:14.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.068][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-04-04 16:02:14.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:14.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.073][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:02:14.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:02:14.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.078][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:02:14.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:02:14.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.083][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-04-04 16:02:14.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-04-04 16:02:14.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.088][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-04-04 16:02:14.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-04-04 16:02:14.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.104][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:14.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:14.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.148][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:14.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:14.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.153][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:14.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:14.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.158][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:14.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:14.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.199][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.201][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.202][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.203][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.220][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-04-04 16:02:14.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:14.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.229][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-04-04 16:02:14.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:14.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.234][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-04-04 16:02:14.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:14.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.239][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-04-04 16:02:14.241][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:14.242][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.243][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.244][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-04-04 16:02:14.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:14.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.260][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2026-04-04 16:02:14.261][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:14.262][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.264][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.270][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.271][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.273][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.274][ef$get] fields variable is a list.
biodb.INFO [2026-04-04 16:02:14.284][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.286][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-04-04 16:02:14.287][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:14.288][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:14.291][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2026-04-04 16:02:14.296][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2026-04-04 16:02:14.300][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-04-04 16:02:14.301][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:14.303][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-04-04 16:02:14.304][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:14.305][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-04-04 16:02:14.489][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.490][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-04-04 16:02:14.492][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:14.493][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.501][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.503][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-04-04 16:02:14.504][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:14.505][biodb::testThat]
biodb.WARN [2026-04-04 16:02:14.527][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-04-04 16:02:14.552][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-04-04 16:02:14.563][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.565][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-04-04 16:02:14.566][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:14.567][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:14.591][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2026-04-04 16:02:14.661][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2026-04-04 16:02:14.702][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-04-04 16:02:14.704][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:14.705][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-04-04 16:02:14.706][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:14.707][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-04-04 16:02:14.799][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.800][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-04-04 16:02:14.802][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:14.803][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-04-04 16:02:14.867][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.868][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-04-04 16:02:14.870][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:14.871][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.882][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.883][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-04-04 16:02:14.884][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:14.885][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-04-04 16:02:14.945][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.946][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-04-04 16:02:14.947][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:14.948][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.957][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-04-04 16:02:14.958][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2026-04-04 16:02:14.959][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-04-04 16:02:14.961][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:14.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:14.963][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:14.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:14.965][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:14.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-04-04 16:02:14.979][biodb::testContext]
biodb.INFO [2026-04-04 16:02:14.981][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:02:14.982][biodb::testContext] Test context - Gene long tests
biodb.INFO [2026-04-04 16:02:14.983][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:02:14.984][biodb::testContext]
biodb.INFO [2026-04-04 16:02:14.987][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:02:14.989][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-04-04 16:02:14.993][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:14.994][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-04-04 16:02:14.996][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-04-04 16:02:14.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:14.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:14.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.000][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-04-04 16:02:15.007][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-04-04 16:02:15.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.012][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-04-04 16:02:15.013][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-04-04 16:02:15.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.017][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-04-04 16:02:15.019][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-04-04 16:02:15.020][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-04-04 16:02:15.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.025][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-04-04 16:02:15.026][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-04-04 16:02:15.027][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-04-04 16:02:15.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.032][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-04-04 16:02:15.033][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-04-04 16:02:15.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.038][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-04-04 16:02:15.039][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-04-04 16:02:15.040][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-04-04 16:02:15.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.045][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-04-04 16:02:15.046][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-04-04 16:02:15.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.051][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-04-04 16:02:15.052][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-04-04 16:02:15.053][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-04-04 16:02:15.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.058][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:02:15.059][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-04-04 16:02:15.061][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-04-04 16:02:15.062][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-04-04 16:02:15.063][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-04-04 16:02:15.065][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-04-04 16:02:15.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.070][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-04-04 16:02:15.071][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-04-04 16:02:15.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.076][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-04-04 16:02:15.077][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-04-04 16:02:15.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.082][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-04-04 16:02:15.084][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-04-04 16:02:15.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.087][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[2026-04-04 16:02:15.088][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-04-04 16:02:15.090][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-04-04 16:02:15.091][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-04-04 16:02:15.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.096][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:02:15.097][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-04-04 16:02:15.108][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-04-04 16:02:15.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.113][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-04-04 16:02:15.114][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-04-04 16:02:15.115][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-04-04 16:02:15.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.120][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-04-04 16:02:15.122][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:15.123][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-04-04 16:02:15.125][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.126][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:15.127][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.129][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.130][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:15.131][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.132][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:02:15.133][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:15.135][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.136][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-04-04 16:02:15.137][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:15.138][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:15.140][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.141][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:15.141][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:15.141][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:15.141][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:02:15.141][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:02:15.142][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:15.144][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:15.145][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:15.146][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:15.147][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:15.148][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:15.150][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.151][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:15.152][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:15.153][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:15.155][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:15.156][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:15.158][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-04-04 16:02:15.160][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:15.161][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:02:15.162][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.164][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:15.165][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.166][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.167][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:15.169][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.170][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:02:15.171][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:15.172][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.174][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-04-04 16:02:15.175][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:15.176][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:15.178][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.179][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:15.179][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:15.179][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:15.179][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:02:15.179][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:02:15.180][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:15.181][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:15.183][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:15.184][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:15.185][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:15.186][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:15.187][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.189][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:15.190][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:15.191][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:15.192][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:15.193][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:15.195][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-04-04 16:02:15.197][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.199][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-04-04 16:02:15.200][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.201][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:15.203][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.204][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.205][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:15.206][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.208][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:02:15.209][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:15.210][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:15.212][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-04-04 16:02:15.217][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:15.218][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:15.219][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.220][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:15.222][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:15.223][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:15.224][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:15.225][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:15.226][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:15.227][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:15.229][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.230][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:15.231][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:15.232][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:15.233][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:15.235][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:15.236][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-04-04 16:02:15.238][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.239][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:02:15.241][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.242][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:15.243][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.244][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.245][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:15.247][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.248][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:02:15.249][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:15.250][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:15.252][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-04-04 16:02:15.253][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:15.254][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:15.255][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.257][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:15.258][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:15.259][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:15.260][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:15.261][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:15.262][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:15.264][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:15.265][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.266][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:15.267][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:15.268][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:15.270][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:15.271][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:15.272][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:15.274][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.275][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[2026-04-04 16:02:15.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.308][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[2026-04-04 16:02:15.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.353][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[2026-04-04 16:02:15.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.366][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-04-04 16:02:15.368][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-04-04 16:02:15.370][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-04-04 16:02:15.371][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-04-04 16:02:15.373][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-04-04 16:02:15.375][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-04-04 16:02:15.377][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-04-04 16:02:15.379][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-04-04 16:02:15.381][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-04-04 16:02:15.382][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-04-04 16:02:15.384][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-04-04 16:02:15.386][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-04-04 16:02:15.388][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-04-04 16:02:15.390][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-04-04 16:02:15.392][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-04-04 16:02:15.393][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-04-04 16:02:15.395][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-04-04 16:02:15.397][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-04-04 16:02:15.398][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-04-04 16:02:15.400][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-04-04 16:02:15.402][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-04-04 16:02:15.404][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-04-04 16:02:15.405][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-04-04 16:02:15.411][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-04-04 16:02:15.413][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-04-04 16:02:15.415][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-04-04 16:02:15.416][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-04-04 16:02:15.418][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-04-04 16:02:15.420][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-04-04 16:02:15.421][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-04-04 16:02:15.423][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-04-04 16:02:15.425][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-04-04 16:02:15.426][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-04-04 16:02:15.428][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-04-04 16:02:15.430][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-04-04 16:02:15.431][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-04-04 16:02:15.433][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-04-04 16:02:15.435][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-04-04 16:02:15.437][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-04-04 16:02:15.438][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-04-04 16:02:15.440][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-04-04 16:02:15.442][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-04-04 16:02:15.444][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-04-04 16:02:15.445][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-04-04 16:02:15.447][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-04-04 16:02:15.449][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-04-04 16:02:15.451][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-04-04 16:02:15.452][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-04-04 16:02:15.454][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-04-04 16:02:15.456][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-04-04 16:02:15.458][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-04-04 16:02:15.459][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-04-04 16:02:15.461][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-04-04 16:02:15.463][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-04-04 16:02:15.465][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-04-04 16:02:15.466][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-04-04 16:02:15.468][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-04-04 16:02:15.470][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-04-04 16:02:15.471][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-04-04 16:02:15.473][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-04-04 16:02:15.475][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-04-04 16:02:15.477][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-04-04 16:02:15.479][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-04-04 16:02:15.480][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-04-04 16:02:15.482][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-04-04 16:02:15.484][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-04-04 16:02:15.486][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-04-04 16:02:15.487][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-04-04 16:02:15.489][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-04-04 16:02:15.491][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-04-04 16:02:15.492][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-04-04 16:02:15.494][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-04-04 16:02:15.496][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-04-04 16:02:15.498][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-04-04 16:02:15.499][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-04-04 16:02:15.501][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-04-04 16:02:15.503][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-04-04 16:02:15.504][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-04-04 16:02:15.506][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-04-04 16:02:15.508][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-04-04 16:02:15.510][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-04-04 16:02:15.511][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-04-04 16:02:15.513][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-04-04 16:02:15.515][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-04-04 16:02:15.517][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:02:15.518][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:15.519][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.522][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:15.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:15.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:15.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:15.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:15.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:15.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:15.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:15.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:15.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:15.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:15.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:15.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:15.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:15.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:15.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:15.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:15.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:15.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:15.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:15.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:15.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:15.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:15.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:15.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.622][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[2026-04-04 16:02:15.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:15.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:15.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:15.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:15.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:15.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:15.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:15.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:15.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:15.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:15.656][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-04-04 16:02:15.658][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-04-04 16:02:15.660][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.662][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-04-04 16:02:15.663][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.664][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:15.665][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.667][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.668][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.669][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.670][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-04-04 16:02:15.672][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:15.673][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.674][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-04-04 16:02:15.675][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:15.677][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-04-04 16:02:15.677][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-04-04 16:02:15.678][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:15.679][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:15.681][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-04-04 16:02:15.682][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:15.683][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:15.684][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:15.685][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:15.686][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:15.688][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.689][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-04-04 16:02:15.689][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-04-04 16:02:15.690][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:15.691][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:15.692][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.694][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:15.695][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-04-04 16:02:15.697][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.699][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-04-04 16:02:15.700][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.701][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:15.703][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.704][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.705][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.706][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.708][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-04-04 16:02:15.709][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:15.710][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.712][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-04-04 16:02:15.713][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:15.714][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-04-04 16:02:15.714][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-04-04 16:02:15.714][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-04-04 16:02:15.714][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-04-04 16:02:15.714][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-04-04 16:02:15.714][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-04-04 16:02:15.716][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:15.717][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:15.718][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-04-04 16:02:15.719][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:15.720][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:15.722][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:15.723][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:15.724][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:15.725][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.727][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:15.727][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-04-04 16:02:15.728][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:15.729][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:15.730][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.731][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:15.733][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-04-04 16:02:15.735][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:15.737][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-04-04 16:02:15.738][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.739][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:15.741][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.742][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.743][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.744][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.746][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-04-04 16:02:15.747][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:15.748][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.749][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-04-04 16:02:15.751][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:15.752][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-04-04 16:02:15.752][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:15.752][self$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[2026-04-04 16:02:15.752][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:15.752][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:15.752][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:15.752][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:15.752][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:15.752][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:15.752][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:15.752][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-04-04 16:02:15.752][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:15.752][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:15.752][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:15.754][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:15.755][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:15.755][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:15.755][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:15.756][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-04-04 16:02:15.758][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:15.759][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:15.760][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:15.761][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:15.762][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:15.764][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.765][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:15.765][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-04-04 16:02:15.765][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-04-04 16:02:15.766][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:15.767][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:15.768][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.770][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-04-04 16:02:15.771][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-04-04 16:02:15.774][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.775][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-04-04 16:02:15.776][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.778][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:15.779][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.780][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.781][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.783][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.784][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-04-04 16:02:15.785][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:15.787][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.788][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-04-04 16:02:15.789][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:15.790][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-04-04 16:02:15.790][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-04-04 16:02:15.792][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:15.793][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:15.794][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-04-04 16:02:15.795][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:15.801][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:15.802][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:15.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:15.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:15.806][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:15.807][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:15.807][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-04-04 16:02:15.807][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-04-04 16:02:15.808][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:15.809][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:15.811][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:15.812][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-04-04 16:02:15.814][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-04-04 16:02:15.816][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-04-04 16:02:15.817][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-04-04 16:02:15.819][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-04-04 16:02:15.821][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-04-04 16:02:15.823][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-04-04 16:02:15.831][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2026-04-04 16:02:15.870][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2026-04-04 16:02:15.876][biodb::testThat]
biodb.INFO [2026-04-04 16:02:15.877][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-04-04 16:02:15.878][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:15.879][biodb::testThat]
biodb.TRACE[2026-04-04 16:02:15.885][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2026-04-04 16:02:15.887][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2026-04-04 16:02:15.892][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2026-04-04 16:02:15.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-04-04 16:02:15.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:15.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:15.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:15.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:15.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:15.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-04-04 16:02:15.925][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:15.927][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:15.928][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:15.930][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:15.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:15.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:15.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:15.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:15.938][ef$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:15.939][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:15.940][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:15.942][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:15.944][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:15.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:15.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:15.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:15.949][ef$get] Asked field names are: location.
biodb.TRACE[2026-04-04 16:02:15.951][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2026-04-04 16:02:15.952][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:15.953][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:15.955][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2026-04-04 16:02:15.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2026-04-04 16:02:15.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:15.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:15.961][ef$get] Asked field names are: symbol.
biodb.TRACE[2026-04-04 16:02:15.962][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2026-04-04 16:02:15.963][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:15.964][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:15.966][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2026-04-04 16:02:15.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2026-04-04 16:02:15.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:15.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:15.973][ef$get] Asked field names are: synonyms.
biodb.TRACE[2026-04-04 16:02:15.974][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:15.975][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:15.976][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:15.979][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2026-04-04 16:02:15.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:15.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:15.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:15.985][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2026-04-04 16:02:15.987][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2026-04-04 16:02:15.989][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:15.991][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:15.994][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2026-04-04 16:02:15.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2026-04-04 16:02:15.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:15.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:16.005][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:16.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:16.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:16.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:16.011][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-04-04 16:02:16.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-04-04 16:02:16.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:16.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:16.017][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-04-04 16:02:16.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-04-04 16:02:16.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:16.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:16.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:16.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:16.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:16.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:16.027][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-04-04 16:02:16.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-04-04 16:02:16.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:16.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:16.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:16.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:16.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:16.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:16.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:16.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:16.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:16.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:16.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:16.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:16.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:16.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:16.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:16.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:16.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:16.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:16.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:16.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:16.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:16.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:16.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:16.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:16.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:16.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-04-04 16:02:16.070][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2026-04-04 16:02:16.072][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-04-04 16:02:16.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:16.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:16.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:16.078][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-04-04 16:02:16.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:16.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:16.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:16.083][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:16.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:16.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:16.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:16.088][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:16.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:16.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:16.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:16.093][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:16.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:16.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:16.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-04-04 16:02:16.098][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2026-04-04 16:02:16.138][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2026-04-04 16:02:16.158][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2026-04-04 16:02:16.159][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2026-04-04 16:02:16.165][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2026-04-04 16:02:16.167][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-04-04 16:02:16.168][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:16.169][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-04-04 16:02:16.171][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:16.172][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-04-04 16:02:16.236][biodb::testThat]
biodb.INFO [2026-04-04 16:02:16.237][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-04-04 16:02:16.239][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:16.240][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:16.243][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2026-04-04 16:02:16.244][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2026-04-04 16:02:16.246][cch$loadContents] Load 8 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-04-04 16:02:16.248][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:16.249][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:16.251][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:16.252][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-04-04 16:02:16.253][private$retrieveContents] Get entry content(s) for 8 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-04-04 16:02:16.312][biodb::testThat]
biodb.INFO [2026-04-04 16:02:16.313][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-04-04 16:02:16.315][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:16.316][biodb::testThat]
biodb.TRACE[2026-04-04 16:02:16.320][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:16.322][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:16.323][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:16.325][ef$get] fields variable is a list.
biodb.DEBUG[2026-04-04 16:02:16.326][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2026-04-04 16:02:16.338][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-04-04 16:02:16.339][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-04-04 16:02:16.342][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-04-04 16:02:16.343][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:16.345][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:16.347][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:16.349][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-04-04 16:02:16.377][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-04-04 16:02:16.460][biodb::testThat]
biodb.INFO [2026-04-04 16:02:16.462][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-04-04 16:02:16.463][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:16.464][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:16.474][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-04-04 16:02:16.475][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-04-04 16:02:16.477][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-04-04 16:02:16.478][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:16.479][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:16.481][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:16.482][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-04-04 16:02:16.483][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-04-04 16:02:16.541][biodb::testThat]
biodb.INFO [2026-04-04 16:02:16.542][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-04-04 16:02:16.544][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:16.545][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:16.550][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-04-04 16:02:16.552][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-04-04 16:02:16.554][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-04-04 16:02:16.555][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:16.557][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:16.558][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:16.559][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-04-04 16:02:16.560][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-04-04 16:02:16.623][biodb::testThat]
biodb.INFO [2026-04-04 16:02:16.625][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-04-04 16:02:16.626][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:16.627][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-04-04 16:02:16.684][biodb::testThat]
biodb.INFO [2026-04-04 16:02:16.685][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-04-04 16:02:16.686][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:16.688][biodb::testThat]
biodb.INFO [2026-04-04 16:02:16.698][biodb::testThat]
biodb.INFO [2026-04-04 16:02:16.699][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-04-04 16:02:16.701][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:16.702][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-04-04 16:02:16.763][biodb::testThat]
biodb.INFO [2026-04-04 16:02:16.764][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-04-04 16:02:16.766][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:16.767][biodb::testThat]
biodb.INFO [2026-04-04 16:02:16.775][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-04-04 16:02:16.777][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2026-04-04 16:02:16.778][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2026-04-04 16:02:16.779][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-04-04 16:02:16.780][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:16.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:16.782][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:16.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:16.784][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:16.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-04-04 16:02:16.790][biodb::testContext]
biodb.INFO [2026-04-04 16:02:16.792][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:02:16.793][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2026-04-04 16:02:16.794][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:02:16.795][biodb::testContext]
biodb.INFO [2026-04-04 16:02:16.797][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:02:16.799][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-04-04 16:02:16.804][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:16.805][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-04-04 16:02:16.806][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-04-04 16:02:16.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:16.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:16.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:16.811][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-04-04 16:02:16.812][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-04-04 16:02:16.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:16.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:16.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:16.816][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-04-04 16:02:16.818][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-04-04 16:02:16.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:16.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:16.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:16.822][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-04-04 16:02:16.823][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-04-04 16:02:16.825][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-04-04 16:02:16.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:16.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:16.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:16.829][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-04-04 16:02:16.830][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-04-04 16:02:16.832][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-04-04 16:02:16.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:16.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:16.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:16.836][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-04-04 16:02:16.838][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-04-04 16:02:16.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:16.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:16.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:16.842][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-04-04 16:02:16.843][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-04-04 16:02:16.845][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-04-04 16:02:16.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:16.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:16.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:16.849][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-04-04 16:02:16.850][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-04-04 16:02:16.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:16.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:16.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:16.855][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-04-04 16:02:16.856][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-04-04 16:02:16.857][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-04-04 16:02:16.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:16.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:16.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:16.862][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:02:16.863][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-04-04 16:02:16.864][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-04-04 16:02:16.866][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-04-04 16:02:16.867][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-04-04 16:02:16.868][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-04-04 16:02:16.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:16.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:16.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:16.872][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-04-04 16:02:16.874][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-04-04 16:02:16.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:16.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:16.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:16.878][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-04-04 16:02:16.879][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-04-04 16:02:16.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:16.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:16.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:16.884][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-04-04 16:02:16.885][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-04-04 16:02:16.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:16.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:16.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:16.890][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-04-04 16:02:16.891][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-04-04 16:02:16.892][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-04-04 16:02:16.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:16.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:16.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:16.897][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:02:16.898][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-04-04 16:02:16.908][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-04-04 16:02:16.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:16.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:16.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:16.913][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-04-04 16:02:16.914][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-04-04 16:02:16.916][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-04-04 16:02:16.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:16.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:16.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:16.926][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-04-04 16:02:16.928][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:16.929][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-04-04 16:02:16.931][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:16.932][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:16.933][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:16.935][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:16.936][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:16.937][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:16.938][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:02:16.940][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:16.941][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:16.942][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-04-04 16:02:16.944][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:16.945][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:16.946][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:16.948][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:16.948][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:16.948][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:16.948][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:02:16.948][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:02:16.949][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:16.951][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:16.952][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:16.953][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:16.954][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:16.956][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:16.957][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:16.958][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:16.959][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:16.961][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:16.962][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:16.963][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:16.965][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-04-04 16:02:16.967][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:16.968][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:02:16.970][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:16.971][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:16.972][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:16.974][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:16.975][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:16.977][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:16.978][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:02:16.979][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:16.981][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:16.982][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-04-04 16:02:16.984][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:16.985][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:16.986][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:16.988][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:16.988][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:16.988][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:16.988][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:02:16.988][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:02:16.989][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:16.990][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:16.991][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:16.992][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:16.994][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:16.995][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:16.996][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:16.997][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:16.998][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:17.000][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:17.001][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:17.002][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:17.004][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-04-04 16:02:17.007][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.008][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-04-04 16:02:17.009][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.012][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:17.014][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.017][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:17.021][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:17.023][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:17.025][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:02:17.028][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:17.030][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:17.033][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-04-04 16:02:17.035][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:17.038][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:17.040][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.043][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:17.045][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:17.048][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:17.050][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:17.052][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:17.054][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:17.057][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:17.059][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:17.062][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:17.064][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:17.066][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:17.069][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:17.072][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:17.074][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-04-04 16:02:17.079][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.081][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:02:17.084][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.086][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:17.089][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.091][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:17.094][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:17.096][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:17.098][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:02:17.100][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:17.102][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:17.104][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-04-04 16:02:17.106][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:17.108][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:17.111][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.113][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:17.115][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:17.118][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:17.119][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:17.121][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:17.123][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:17.125][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:17.127][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:17.130][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:17.132][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:17.134][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:17.136][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:17.139][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:17.142][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:17.144][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.146][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[2026-04-04 16:02:17.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.157][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[2026-04-04 16:02:17.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.178][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[2026-04-04 16:02:17.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.239][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[2026-04-04 16:02:17.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.251][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[2026-04-04 16:02:17.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.258][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-04-04 16:02:17.259][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-04-04 16:02:17.261][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-04-04 16:02:17.263][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-04-04 16:02:17.264][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-04-04 16:02:17.266][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-04-04 16:02:17.268][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-04-04 16:02:17.269][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-04-04 16:02:17.271][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-04-04 16:02:17.273][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-04-04 16:02:17.275][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-04-04 16:02:17.276][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-04-04 16:02:17.278][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-04-04 16:02:17.280][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-04-04 16:02:17.282][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-04-04 16:02:17.284][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-04-04 16:02:17.285][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-04-04 16:02:17.287][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-04-04 16:02:17.289][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-04-04 16:02:17.291][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-04-04 16:02:17.292][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-04-04 16:02:17.294][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-04-04 16:02:17.296][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-04-04 16:02:17.298][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-04-04 16:02:17.299][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-04-04 16:02:17.301][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-04-04 16:02:17.303][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-04-04 16:02:17.304][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-04-04 16:02:17.306][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-04-04 16:02:17.308][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-04-04 16:02:17.309][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-04-04 16:02:17.311][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-04-04 16:02:17.313][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-04-04 16:02:17.315][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-04-04 16:02:17.316][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-04-04 16:02:17.318][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-04-04 16:02:17.320][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-04-04 16:02:17.321][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-04-04 16:02:17.323][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-04-04 16:02:17.325][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-04-04 16:02:17.326][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-04-04 16:02:17.328][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-04-04 16:02:17.330][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-04-04 16:02:17.331][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-04-04 16:02:17.333][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-04-04 16:02:17.335][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-04-04 16:02:17.337][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-04-04 16:02:17.338][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-04-04 16:02:17.340][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-04-04 16:02:17.342][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-04-04 16:02:17.343][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-04-04 16:02:17.345][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-04-04 16:02:17.347][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-04-04 16:02:17.349][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-04-04 16:02:17.350][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-04-04 16:02:17.352][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-04-04 16:02:17.354][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-04-04 16:02:17.357][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-04-04 16:02:17.358][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-04-04 16:02:17.360][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-04-04 16:02:17.362][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-04-04 16:02:17.364][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-04-04 16:02:17.369][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-04-04 16:02:17.371][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-04-04 16:02:17.373][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-04-04 16:02:17.375][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-04-04 16:02:17.376][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-04-04 16:02:17.378][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-04-04 16:02:17.380][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-04-04 16:02:17.381][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-04-04 16:02:17.383][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-04-04 16:02:17.385][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-04-04 16:02:17.386][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-04-04 16:02:17.388][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-04-04 16:02:17.390][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-04-04 16:02:17.391][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-04-04 16:02:17.393][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-04-04 16:02:17.395][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-04-04 16:02:17.397][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-04-04 16:02:17.398][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-04-04 16:02:17.400][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-04-04 16:02:17.402][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-04-04 16:02:17.404][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-04-04 16:02:17.405][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-04-04 16:02:17.407][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:02:17.408][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:17.409][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.412][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:17.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:17.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:17.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:17.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:17.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:17.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:17.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:17.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:17.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:17.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:17.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:17.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:17.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:17.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.468][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[2026-04-04 16:02:17.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:17.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:17.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:17.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:17.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:17.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:17.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:17.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:17.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.501][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[2026-04-04 16:02:17.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:17.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:17.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:17.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:17.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:17.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:17.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.524][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[2026-04-04 16:02:17.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:17.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:17.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:17.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:17.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:17.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:17.542][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-04-04 16:02:17.544][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-04-04 16:02:17.551][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.552][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-04-04 16:02:17.553][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.554][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:17.556][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.557][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:17.558][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.559][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:17.561][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-04-04 16:02:17.562][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:17.563][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.564][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-04-04 16:02:17.566][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:17.567][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-04-04 16:02:17.567][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-04-04 16:02:17.568][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:17.569][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:17.571][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-04-04 16:02:17.572][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:17.573][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:17.574][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:17.575][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:17.576][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:17.578][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:17.579][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-04-04 16:02:17.579][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-04-04 16:02:17.580][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:17.581][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:17.582][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.584][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:17.585][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-04-04 16:02:17.587][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.589][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-04-04 16:02:17.590][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.591][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:17.592][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.594][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:17.595][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.596][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:17.597][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-04-04 16:02:17.599][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:17.600][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.601][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-04-04 16:02:17.602][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:17.604][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-04-04 16:02:17.604][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-04-04 16:02:17.604][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-04-04 16:02:17.604][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-04-04 16:02:17.604][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-04-04 16:02:17.604][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-04-04 16:02:17.605][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:17.606][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:17.608][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-04-04 16:02:17.609][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:17.610][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:17.611][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:17.612][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:17.613][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:17.615][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:17.616][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:17.616][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-04-04 16:02:17.617][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:17.618][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:17.619][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.621][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:17.622][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-04-04 16:02:17.625][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:17.626][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-04-04 16:02:17.627][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.628][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:17.629][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.631][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:17.632][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.633][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:17.634][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-04-04 16:02:17.636][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:17.637][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.638][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-04-04 16:02:17.639][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:17.641][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-04-04 16:02:17.641][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:17.641][self$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[2026-04-04 16:02:17.641][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:17.641][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:17.641][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:17.641][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:17.641][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:17.641][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:17.641][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:17.641][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-04-04 16:02:17.641][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:17.641][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:17.641][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:17.642][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:17.643][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:17.643][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:17.643][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:17.645][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-04-04 16:02:17.646][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:17.647][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:17.648][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:17.649][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:17.650][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:17.652][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:17.653][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:17.653][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-04-04 16:02:17.653][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-04-04 16:02:17.654][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:17.655][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:17.656][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.658][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-04-04 16:02:17.659][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-04-04 16:02:17.662][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.663][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-04-04 16:02:17.664][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.665][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:17.667][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.668][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:17.669][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.670][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:17.671][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-04-04 16:02:17.673][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:17.674][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.675][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-04-04 16:02:17.676][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:17.678][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-04-04 16:02:17.678][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-04-04 16:02:17.679][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:17.680][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:17.681][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-04-04 16:02:17.683][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:17.684][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:17.685][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:17.686][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:17.687][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:17.688][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:17.689][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:17.689][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-04-04 16:02:17.689][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-04-04 16:02:17.691][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:17.692][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:17.693][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:17.694][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-04-04 16:02:17.696][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-04-04 16:02:17.698][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-04-04 16:02:17.699][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-04-04 16:02:17.701][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-04-04 16:02:17.703][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-04-04 16:02:17.705][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-04-04 16:02:17.713][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2026-04-04 16:02:17.718][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2026-04-04 16:02:17.728][biodb::testThat]
biodb.INFO [2026-04-04 16:02:17.729][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-04-04 16:02:17.730][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:17.731][biodb::testThat]
biodb.TRACE[2026-04-04 16:02:17.735][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2026-04-04 16:02:17.736][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2026-04-04 16:02:17.740][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2026-04-04 16:02:17.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-04-04 16:02:17.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:17.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:17.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:17.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:17.756][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:17.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-04-04 16:02:17.778][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:17.781][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:17.786][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:17.790][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:17.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:17.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:17.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:17.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:17.821][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:17.847][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:17.850][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:17.853][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:17.857][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:17.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:17.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:17.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:17.867][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:17.870][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:17.872][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:17.874][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:17.877][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:17.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:17.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:17.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:17.886][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:17.888][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:17.891][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:17.893][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:17.896][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:17.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:17.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:17.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:17.906][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:17.908][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:17.910][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:17.913][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:17.915][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:17.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:17.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:17.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:17.925][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:17.928][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:17.930][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:17.932][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:17.935][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:17.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:17.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:17.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:17.944][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-04-04 16:02:17.946][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:17.949][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:17.951][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:17.954][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-04-04 16:02:17.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:17.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:17.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:17.964][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:17.966][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:17.968][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:17.971][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:17.974][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:17.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:17.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:17.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:17.983][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:17.985][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:17.987][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:17.990][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:17.993][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:17.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:17.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.003][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:18.005][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:18.008][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.010][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.013][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:18.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:18.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.023][ef$get] Asked field names are: logp.
biodb.TRACE[2026-04-04 16:02:18.026][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-04-04 16:02:18.028][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.030][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.033][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-04-04 16:02:18.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-04-04 16:02:18.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.043][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-04-04 16:02:18.045][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:18.047][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.050][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-04-04 16:02:18.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:18.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.063][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:18.065][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:18.067][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.069][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.072][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:18.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:18.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.082][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:18.085][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:18.087][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.090][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.093][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:18.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:18.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.102][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2026-04-04 16:02:18.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:18.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.122][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:18.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:18.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.131][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:18.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:18.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.140][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2026-04-04 16:02:18.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:18.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.147][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:18.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:18.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.152][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:18.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:18.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.159][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2026-04-04 16:02:18.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:18.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.164][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:18.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:18.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.169][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:18.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:18.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.174][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2026-04-04 16:02:18.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:18.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.179][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:18.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:18.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.184][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:18.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:18.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.189][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2026-04-04 16:02:18.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:18.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.195][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:18.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:18.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.200][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:18.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:18.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.205][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:18.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:18.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.210][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:18.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:18.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.215][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:18.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:18.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.225][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:18.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:18.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-04-04 16:02:18.261][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2026-04-04 16:02:18.263][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-04-04 16:02:18.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:18.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.268][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-04-04 16:02:18.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:18.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.273][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:18.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:18.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.279][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:02:18.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:02:18.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.284][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:02:18.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:02:18.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.289][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-04-04 16:02:18.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-04-04 16:02:18.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.294][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-04-04 16:02:18.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-04-04 16:02:18.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.335][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:18.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:18.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.379][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:18.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:18.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.384][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:18.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:18.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.389][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:18.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:18.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.417][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.418][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.419][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.421][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.437][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-04-04 16:02:18.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:18.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:18.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:18.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:18.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:18.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.452][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-04-04 16:02:18.453][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:18.455][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.456][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.457][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-04-04 16:02:18.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:18.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.472][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-04-04 16:02:18.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:18.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:18.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:18.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:18.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:18.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.488][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-04-04 16:02:18.489][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:18.490][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.491][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.493][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-04-04 16:02:18.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:18.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.513][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:18.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:18.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.518][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:18.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:18.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.523][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:18.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:18.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.529][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:18.530][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:18.531][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.533][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.534][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:18.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:18.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.550][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-04-04 16:02:18.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-04-04 16:02:18.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.555][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-04-04 16:02:18.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-04-04 16:02:18.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.560][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-04-04 16:02:18.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-04-04 16:02:18.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.565][ef$get] Asked field names are: logp.
biodb.TRACE[2026-04-04 16:02:18.566][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-04-04 16:02:18.568][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.569][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.570][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-04-04 16:02:18.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-04-04 16:02:18.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.586][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:18.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:18.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.591][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:18.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:18.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.596][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:18.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:18.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.601][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:18.603][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:18.604][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.605][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.606][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:18.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:18.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.623][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:18.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:18.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.628][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:18.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:18.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.633][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:18.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:18.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.638][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:18.640][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:18.641][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.642][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.644][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:18.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:18.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.659][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:18.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:18.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.664][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:18.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:18.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.669][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:18.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:18.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.674][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:18.676][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:18.677][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.678][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.679][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:18.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:18.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.700][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:18.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:18.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.706][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:18.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:18.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.711][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:18.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:18.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.716][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:18.717][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:18.718][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.719][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.721][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:18.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:18.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.736][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:18.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:18.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.741][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:18.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:18.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.746][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:18.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:18.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.751][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:18.753][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:18.754][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.755][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.756][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:18.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:18.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.771][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:18.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:18.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.777][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:18.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:18.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.782][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:18.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:18.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.787][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:18.788][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:18.789][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.790][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.792][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:18.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:18.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.807][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:18.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:18.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.813][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:18.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:18.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.818][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:18.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:18.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.823][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:18.824][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:18.826][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.827][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.828][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:18.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:18.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.844][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:18.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:18.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.850][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:18.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:18.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.855][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:18.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:18.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.860][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:18.862][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:18.863][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.864][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.865][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:18.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:18.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.886][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:18.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:18.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.891][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:18.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:18.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:18.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:18.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.902][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:18.903][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:18.904][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.906][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.907][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:18.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:18.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.923][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:18.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:18.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.928][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:18.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:18.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.933][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:18.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:18.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.938][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:18.940][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:18.941][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.942][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.943][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:18.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:18.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.959][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:18.961][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:18.962][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.963][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.970][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:18.971][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:18.973][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.974][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.981][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:18.982][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:18.983][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.985][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:18.992][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:18.993][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:18.995][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:18.996][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.003][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:19.005][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:19.006][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.007][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.014][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:19.016][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:19.017][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.018][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.025][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:19.026][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:19.028][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.029][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.036][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:19.037][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:19.039][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.040][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.047][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:19.048][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:19.049][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.050][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.057][ef$get] Asked field names are: logp.
biodb.TRACE[2026-04-04 16:02:19.058][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-04-04 16:02:19.059][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.061][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.067][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:19.069][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:19.070][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.071][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.078][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:19.084][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:19.085][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.087][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.093][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:19.095][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:19.096][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.097][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.103][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:19.105][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:19.106][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.107][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.114][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:19.115][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:19.116][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.117][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.124][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2026-04-04 16:02:19.126][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2026-04-04 16:02:19.128][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2026-04-04 16:02:19.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-04-04 16:02:19.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:19.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:19.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:19.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:19.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:19.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-04-04 16:02:19.145][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.147][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.148][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.149][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.157][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.158][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.160][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.161][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.162][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.167][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.169][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.170][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.171][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.173][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.178][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.179][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.181][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.182][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.183][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.188][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:19.190][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:19.191][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.192][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.194][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:19.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:19.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.199][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:19.200][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:19.202][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.203][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.204][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:19.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:19.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.210][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-04-04 16:02:19.211][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:19.212][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.213][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.215][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-04-04 16:02:19.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:19.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.220][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:19.222][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:19.223][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.224][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.226][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:19.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:19.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.231][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:19.232][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:19.233][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.235][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.236][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:19.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:19.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.241][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:19.243][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:19.244][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.245][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:19.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:19.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.252][ef$get] Asked field names are: logp.
biodb.TRACE[2026-04-04 16:02:19.253][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-04-04 16:02:19.255][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.256][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.257][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-04-04 16:02:19.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-04-04 16:02:19.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.263][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-04-04 16:02:19.264][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:19.265][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.266][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-04-04 16:02:19.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:19.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.278][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:19.280][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:19.281][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.282][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.284][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:19.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:19.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.289][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:19.290][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:19.291][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.293][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.294][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:19.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:19.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.300][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2026-04-04 16:02:19.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.305][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.310][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.315][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2026-04-04 16:02:19.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.320][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.325][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.330][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2026-04-04 16:02:19.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:19.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.335][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:19.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:19.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.340][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:19.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:19.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.346][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2026-04-04 16:02:19.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:19.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.351][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:19.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:19.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.356][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:19.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:19.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.361][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2026-04-04 16:02:19.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.367][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.372][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.377][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:19.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:19.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.383][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:19.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:19.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.388][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:19.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:19.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.398][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:19.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:19.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-04-04 16:02:19.436][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2026-04-04 16:02:19.438][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-04-04 16:02:19.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:19.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.444][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-04-04 16:02:19.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:19.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.449][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:19.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:19.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.454][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:02:19.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:02:19.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.464][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:02:19.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:02:19.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.469][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-04-04 16:02:19.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-04-04 16:02:19.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.474][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-04-04 16:02:19.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-04-04 16:02:19.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.491][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:19.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:19.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.535][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:19.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:19.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.540][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:19.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:19.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.545][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:19.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:19.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.573][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.575][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.576][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.577][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:19.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:19.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:19.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:19.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:19.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:19.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:19.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:19.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.610][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:19.611][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:19.613][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.614][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:19.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:19.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:19.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:19.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:19.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:19.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:19.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:19.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.652][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:19.653][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:19.655][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.656][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:19.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:19.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.673][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:19.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:19.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.678][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:19.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:19.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.683][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:19.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:19.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.688][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:19.690][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:19.691][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.692][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.693][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:19.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:19.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.709][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-04-04 16:02:19.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-04-04 16:02:19.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.714][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-04-04 16:02:19.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-04-04 16:02:19.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.719][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-04-04 16:02:19.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-04-04 16:02:19.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.724][ef$get] Asked field names are: logp.
biodb.TRACE[2026-04-04 16:02:19.726][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-04-04 16:02:19.727][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.728][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.729][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-04-04 16:02:19.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-04-04 16:02:19.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.745][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:19.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:19.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.750][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:19.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:19.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.755][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:19.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:19.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.760][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:19.762][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:19.763][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.764][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.765][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:19.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:19.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.781][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:19.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:19.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.787][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:19.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:19.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.792][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:19.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:19.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.798][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:19.799][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:19.800][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.802][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.803][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:19.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:19.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.820][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:19.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:19.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.826][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:19.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:19.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.837][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:19.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:19.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.843][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:19.845][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:19.846][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.847][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.848][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:19.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:19.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:19.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:19.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.869][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:19.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:19.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.874][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:19.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:19.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.880][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:19.881][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:19.882][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.883][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.884][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:19.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:19.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.900][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.905][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.910][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.915][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.916][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.917][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.919][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.920][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:19.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.935][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.940][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.945][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.950][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.952][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.953][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.954][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.955][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:19.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.971][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.976][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.981][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.986][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.988][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.989][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.990][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:19.991][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:19.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:19.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.007][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:20.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:20.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.012][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:20.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:20.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.022][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:20.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:20.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.027][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:20.029][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:20.030][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.031][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.032][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:20.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:20.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.048][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:20.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:20.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.053][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:20.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:20.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.058][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:20.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:20.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.063][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:20.065][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:20.066][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.067][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.068][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:20.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:20.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.084][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:20.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:20.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.089][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:20.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:20.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.094][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:20.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:20.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.099][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:20.101][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:20.102][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.103][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.105][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:20.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:20.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.120][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:20.122][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:20.123][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.124][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.131][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:20.132][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-04-04 16:02:20.133][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.135][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.141][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:20.143][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-04-04 16:02:20.144][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.145][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.152][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:20.153][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-04-04 16:02:20.154][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.155][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.162][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:20.164][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:20.165][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.166][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.173][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:20.174][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:20.175][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.176][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.183][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:20.185][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:20.186][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.187][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.194][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:20.195][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:20.197][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.198][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.204][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:20.206][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:20.207][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.213][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.220][ef$get] Asked field names are: logp.
biodb.TRACE[2026-04-04 16:02:20.221][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-04-04 16:02:20.222][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.223][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.230][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:20.231][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:20.233][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.234][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.240][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:20.242][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:20.243][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.244][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.251][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:20.253][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:20.254][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.255][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.262][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:20.263][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-04-04 16:02:20.265][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.266][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.272][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:20.274][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-04-04 16:02:20.275][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.276][ef$get] fields variable is a list.
biodb.INFO [2026-04-04 16:02:20.287][biodb::testThat]
biodb.INFO [2026-04-04 16:02:20.288][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-04-04 16:02:20.289][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:20.290][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:20.293][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-04-04 16:02:20.298][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-04-04 16:02:20.300][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-04-04 16:02:20.301][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:20.303][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:20.304][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:20.305][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-04-04 16:02:20.306][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-04-04 16:02:20.363][biodb::testThat]
biodb.INFO [2026-04-04 16:02:20.364][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-04-04 16:02:20.366][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:20.367][biodb::testThat]
biodb.TRACE[2026-04-04 16:02:20.371][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:20.373][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:20.375][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.376][ef$get] fields variable is a list.
biodb.DEBUG[2026-04-04 16:02:20.378][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2026-04-04 16:02:20.390][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-04-04 16:02:20.391][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-04-04 16:02:20.393][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-04-04 16:02:20.399][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:20.400][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:20.402][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:20.403][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-04-04 16:02:20.404][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-04-04 16:02:20.461][biodb::testThat]
biodb.INFO [2026-04-04 16:02:20.462][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-04-04 16:02:20.464][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:20.465][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:20.475][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-04-04 16:02:20.476][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-04-04 16:02:20.478][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-04-04 16:02:20.479][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:20.481][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:20.482][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:20.483][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-04-04 16:02:20.484][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-04-04 16:02:20.541][biodb::testThat]
biodb.INFO [2026-04-04 16:02:20.543][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-04-04 16:02:20.544][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:20.545][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:20.550][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-04-04 16:02:20.551][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-04-04 16:02:20.553][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-04-04 16:02:20.555][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:20.561][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:20.563][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:20.564][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-04-04 16:02:20.566][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-04-04 16:02:20.622][biodb::testThat]
biodb.INFO [2026-04-04 16:02:20.624][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-04-04 16:02:20.625][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:20.626][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-04-04 16:02:20.683][biodb::testThat]
biodb.INFO [2026-04-04 16:02:20.684][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-04-04 16:02:20.686][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:20.687][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-04-04 16:02:20.747][biodb::testThat]
biodb.INFO [2026-04-04 16:02:20.749][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-04-04 16:02:20.750][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:20.751][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-04-04 16:02:20.808][biodb::testThat]
biodb.INFO [2026-04-04 16:02:20.809][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-04-04 16:02:20.810][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:20.811][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2026-04-04 16:02:20.884][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:20.885][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:20.887][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.888][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:20.889][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:20.890][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:20.892][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:20.893][ef$get] fields variable is a list.
biodb.INFO [2026-04-04 16:02:20.895][biodb::testThat]
biodb.INFO [2026-04-04 16:02:20.896][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2026-04-04 16:02:20.897][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:20.899][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:20.908][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-04-04 16:02:20.909][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-04-04 16:02:20.911][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-04-04 16:02:20.912][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:20.914][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:20.915][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:20.916][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-04-04 16:02:20.918][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-04-04 16:02:20.974][biodb::testThat]
biodb.INFO [2026-04-04 16:02:20.976][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2026-04-04 16:02:20.977][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:20.978][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:20.982][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-04-04 16:02:20.983][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-04-04 16:02:20.985][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-04-04 16:02:20.987][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:20.989][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:20.990][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:20.991][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-04-04 16:02:20.992][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-04-04 16:02:21.055][biodb::testThat]
biodb.INFO [2026-04-04 16:02:21.056][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2026-04-04 16:02:21.057][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:21.058][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:21.062][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-04-04 16:02:21.063][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-04-04 16:02:21.065][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-04-04 16:02:21.066][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:21.068][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:21.069][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:21.070][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-04-04 16:02:21.071][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-04-04 16:02:21.129][biodb::testThat]
biodb.INFO [2026-04-04 16:02:21.131][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2026-04-04 16:02:21.132][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:21.133][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:21.137][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-04-04 16:02:21.138][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-04-04 16:02:21.140][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-04-04 16:02:21.142][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:21.143][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:21.145][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:21.146][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-04-04 16:02:21.147][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2026-04-04 16:02:21.211][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:21.213][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:21.214][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:21.215][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:21.216][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:21.218][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:21.219][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:21.220][ef$get] fields variable is a list.
biodb.INFO [2026-04-04 16:02:21.222][biodb::testThat]
biodb.INFO [2026-04-04 16:02:21.223][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2026-04-04 16:02:21.225][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:21.226][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:21.230][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-04-04 16:02:21.231][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-04-04 16:02:21.233][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-04-04 16:02:21.234][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:21.236][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:21.237][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:21.239][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-04-04 16:02:21.240][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-04-04 16:02:21.299][biodb::testThat]
biodb.INFO [2026-04-04 16:02:21.300][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2026-04-04 16:02:21.301][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:21.303][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:21.306][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-04-04 16:02:21.308][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-04-04 16:02:21.310][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-04-04 16:02:21.311][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:21.312][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:21.314][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:21.315][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-04-04 16:02:21.316][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-04-04 16:02:21.379][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-04-04 16:02:21.381][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2026-04-04 16:02:21.382][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-04-04 16:02:21.383][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:21.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:21.385][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.388][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-04-04 16:02:21.394][biodb::testContext]
biodb.INFO [2026-04-04 16:02:21.395][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:02:21.396][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2026-04-04 16:02:21.397][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:02:21.399][biodb::testContext]
biodb.INFO [2026-04-04 16:02:21.401][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:02:21.403][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-04-04 16:02:21.408][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:21.409][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-04-04 16:02:21.411][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-04-04 16:02:21.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.415][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-04-04 16:02:21.416][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-04-04 16:02:21.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.421][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-04-04 16:02:21.422][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-04-04 16:02:21.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.426][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[2026-04-04 16:02:21.427][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-04-04 16:02:21.428][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-04-04 16:02:21.429][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-04-04 16:02:21.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.434][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-04-04 16:02:21.435][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-04-04 16:02:21.437][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-04-04 16:02:21.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.441][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-04-04 16:02:21.443][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-04-04 16:02:21.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.447][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-04-04 16:02:21.449][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-04-04 16:02:21.450][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-04-04 16:02:21.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.455][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-04-04 16:02:21.456][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-04-04 16:02:21.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.461][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-04-04 16:02:21.462][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-04-04 16:02:21.463][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-04-04 16:02:21.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.467][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[2026-04-04 16:02:21.468][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:02:21.469][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-04-04 16:02:21.470][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-04-04 16:02:21.472][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-04-04 16:02:21.473][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-04-04 16:02:21.474][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-04-04 16:02:21.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.479][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-04-04 16:02:21.480][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-04-04 16:02:21.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.485][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-04-04 16:02:21.487][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-04-04 16:02:21.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.492][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-04-04 16:02:21.493][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-04-04 16:02:21.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.498][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-04-04 16:02:21.499][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-04-04 16:02:21.500][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-04-04 16:02:21.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.505][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:02:21.506][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-04-04 16:02:21.517][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-04-04 16:02:21.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.522][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-04-04 16:02:21.523][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-04-04 16:02:21.525][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-04-04 16:02:21.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.529][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-04-04 16:02:21.532][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:21.533][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-04-04 16:02:21.539][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:21.541][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:21.542][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:21.544][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:21.545][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:21.546][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:21.547][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:02:21.549][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:21.550][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:21.551][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-04-04 16:02:21.552][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:21.554][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:21.555][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:21.556][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:21.556][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:21.556][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:21.556][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:02:21.556][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:02:21.558][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:21.559][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:21.560][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:21.561][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:21.562][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:21.563][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:21.565][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:21.566][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:21.567][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:21.568][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:21.570][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:21.571][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:21.572][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-04-04 16:02:21.575][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:21.576][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:02:21.577][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:21.578][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:21.580][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:21.581][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:21.582][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:21.583][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:21.585][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:02:21.586][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:21.587][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:21.588][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-04-04 16:02:21.590][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:21.591][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:21.592][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:21.593][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:21.593][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:21.593][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:21.593][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:02:21.593][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:02:21.595][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:21.596][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:21.597][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:21.598][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:21.600][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:21.601][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:21.602][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:21.603][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:21.604][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:21.606][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:21.607][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:21.608][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:21.610][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-04-04 16:02:21.612][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:21.613][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-04-04 16:02:21.614][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:21.615][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:21.617][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:21.618][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:21.619][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:21.620][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:21.622][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:02:21.623][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:21.624][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:21.626][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-04-04 16:02:21.627][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:21.628][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:21.630][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:21.631][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:21.632][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:21.633][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:21.635][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:21.636][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:21.637][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:21.639][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:21.640][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:21.641][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:21.642][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:21.643][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:21.645][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:21.646][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:21.647][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-04-04 16:02:21.650][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:21.651][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:02:21.652][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:21.653][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:21.655][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:21.656][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:21.657][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:21.658][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:21.660][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:02:21.661][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:21.662][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:21.663][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-04-04 16:02:21.665][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:21.666][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:21.667][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:21.668][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:21.670][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:21.671][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:21.672][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:21.673][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:21.674][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:21.675][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:21.677][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:21.678][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:21.679][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:21.680][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:21.681][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:21.683][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:21.684][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:21.686][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.742][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[2026-04-04 16:02:21.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.747][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[2026-04-04 16:02:21.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.764][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[2026-04-04 16:02:21.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.781][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-04-04 16:02:21.783][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-04-04 16:02:21.785][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-04-04 16:02:21.787][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-04-04 16:02:21.788][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-04-04 16:02:21.790][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-04-04 16:02:21.792][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-04-04 16:02:21.794][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-04-04 16:02:21.795][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-04-04 16:02:21.797][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-04-04 16:02:21.799][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-04-04 16:02:21.800][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-04-04 16:02:21.802][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-04-04 16:02:21.804][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-04-04 16:02:21.805][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-04-04 16:02:21.807][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-04-04 16:02:21.809][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-04-04 16:02:21.811][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-04-04 16:02:21.812][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-04-04 16:02:21.814][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-04-04 16:02:21.816][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-04-04 16:02:21.818][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-04-04 16:02:21.819][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-04-04 16:02:21.821][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-04-04 16:02:21.823][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-04-04 16:02:21.824][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-04-04 16:02:21.826][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-04-04 16:02:21.828][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-04-04 16:02:21.829][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-04-04 16:02:21.831][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-04-04 16:02:21.833][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-04-04 16:02:21.834][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-04-04 16:02:21.836][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-04-04 16:02:21.838][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-04-04 16:02:21.840][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-04-04 16:02:21.841][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-04-04 16:02:21.843][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-04-04 16:02:21.845][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-04-04 16:02:21.846][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-04-04 16:02:21.848][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-04-04 16:02:21.850][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-04-04 16:02:21.852][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-04-04 16:02:21.853][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-04-04 16:02:21.855][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-04-04 16:02:21.857][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-04-04 16:02:21.859][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-04-04 16:02:21.860][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-04-04 16:02:21.862][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-04-04 16:02:21.864][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-04-04 16:02:21.866][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-04-04 16:02:21.868][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-04-04 16:02:21.875][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-04-04 16:02:21.877][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-04-04 16:02:21.879][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-04-04 16:02:21.881][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-04-04 16:02:21.883][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-04-04 16:02:21.885][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-04-04 16:02:21.886][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-04-04 16:02:21.888][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-04-04 16:02:21.890][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-04-04 16:02:21.891][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-04-04 16:02:21.893][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-04-04 16:02:21.895][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-04-04 16:02:21.896][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-04-04 16:02:21.898][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-04-04 16:02:21.900][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-04-04 16:02:21.901][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-04-04 16:02:21.903][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-04-04 16:02:21.905][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-04-04 16:02:21.906][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-04-04 16:02:21.908][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-04-04 16:02:21.910][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-04-04 16:02:21.911][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-04-04 16:02:21.913][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-04-04 16:02:21.915][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-04-04 16:02:21.917][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-04-04 16:02:21.918][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-04-04 16:02:21.920][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-04-04 16:02:21.922][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-04-04 16:02:21.923][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-04-04 16:02:21.925][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-04-04 16:02:21.927][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-04-04 16:02:21.928][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-04-04 16:02:21.930][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-04-04 16:02:21.932][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:02:21.933][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:21.934][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.936][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:21.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:21.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:21.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:21.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:21.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:21.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:21.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:21.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:21.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:21.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:21.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:21.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:21.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:21.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:21.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.991][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[2026-04-04 16:02:21.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:21.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:21.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:21.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:21.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:21.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:21.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:22.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:22.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:22.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:22.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:22.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:22.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:22.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:22.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:22.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:22.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:22.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:22.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:22.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:22.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:22.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:22.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:22.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:22.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:22.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:22.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:22.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:22.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:22.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:22.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:22.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:22.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:22.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:22.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:22.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:22.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:22.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:22.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:22.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:22.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:22.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:22.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:22.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:22.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:22.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:22.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:22.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:22.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:22.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:22.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:22.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:22.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:22.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:22.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:22.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:22.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:22.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:22.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:22.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:22.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:22.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:22.072][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.DEBUG[2026-04-04 16:02:22.074][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-04-04 16:02:22.076][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-04-04 16:02:22.079][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.080][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-04-04 16:02:22.082][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.083][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:22.084][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.085][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:22.087][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.088][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:22.090][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-04-04 16:02:22.091][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:22.093][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.094][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-04-04 16:02:22.095][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:22.096][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-04-04 16:02:22.096][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-04-04 16:02:22.098][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:22.099][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:22.100][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-04-04 16:02:22.102][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:22.103][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:22.104][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:22.105][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:22.106][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:22.107][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:22.109][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-04-04 16:02:22.109][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-04-04 16:02:22.110][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:22.111][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:22.112][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.114][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:22.115][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-04-04 16:02:22.118][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.119][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-04-04 16:02:22.120][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.121][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:22.123][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.124][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:22.125][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.126][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:22.128][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-04-04 16:02:22.129][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:22.130][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.132][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-04-04 16:02:22.133][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-04-04 16:02:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-04-04 16:02:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-04-04 16:02:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-04-04 16:02:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-04-04 16:02:22.134][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-04-04 16:02:22.136][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:22.137][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:22.138][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-04-04 16:02:22.139][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:22.140][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:22.142][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:22.143][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:22.144][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:22.145][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:22.146][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:22.146][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-04-04 16:02:22.148][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:22.149][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:22.150][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.151][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:22.153][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-04-04 16:02:22.155][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:22.156][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-04-04 16:02:22.157][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.159][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:22.160][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.161][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:22.162][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.164][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:22.165][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-04-04 16:02:22.166][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:22.167][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.168][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-04-04 16:02:22.170][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:22.171][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-04-04 16:02:22.171][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:22.171][self$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[2026-04-04 16:02:22.171][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:22.171][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:22.171][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:22.171][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:22.171][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:22.171][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:22.171][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:22.171][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-04-04 16:02:22.171][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:22.171][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:22.171][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-04-04 16:02:22.173][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:22.174][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:22.174][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:22.174][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:22.175][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-04-04 16:02:22.176][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:22.177][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:22.179][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:22.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:22.181][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:22.182][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:22.183][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:22.183][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-04-04 16:02:22.183][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-04-04 16:02:22.185][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:22.186][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:22.187][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.188][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-04-04 16:02:22.190][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-04-04 16:02:22.192][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.193][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-04-04 16:02:22.194][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.196][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:22.197][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.198][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:22.199][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.201][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:22.202][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-04-04 16:02:22.203][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:22.204][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.205][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-04-04 16:02:22.207][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:22.208][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-04-04 16:02:22.208][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-04-04 16:02:22.209][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:22.215][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:22.217][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-04-04 16:02:22.218][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:22.219][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:22.220][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:22.222][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:22.223][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:22.224][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:22.225][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:22.225][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-04-04 16:02:22.225][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-04-04 16:02:22.227][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:22.228][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:22.229][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:22.230][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-04-04 16:02:22.232][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-04-04 16:02:22.233][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-04-04 16:02:22.235][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-04-04 16:02:22.237][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-04-04 16:02:22.239][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-04-04 16:02:22.241][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-04-04 16:02:22.247][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2026-04-04 16:02:22.251][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2026-04-04 16:02:22.256][biodb::testThat]
biodb.INFO [2026-04-04 16:02:22.258][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-04-04 16:02:22.259][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:22.260][biodb::testThat]
biodb.TRACE[2026-04-04 16:02:22.263][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2026-04-04 16:02:22.265][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2026-04-04 16:02:22.268][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2026-04-04 16:02:22.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-04-04 16:02:22.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:22.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:22.278][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:22.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:22.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:22.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-04-04 16:02:22.285][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.286][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.288][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.289][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.295][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:22.297][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:22.298][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.299][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.300][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:22.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:22.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.306][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-04-04 16:02:22.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-04-04 16:02:22.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.310][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-04-04 16:02:22.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-04-04 16:02:22.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.320][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-04-04 16:02:22.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-04-04 16:02:22.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-04-04 16:02:22.355][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2026-04-04 16:02:22.358][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-04-04 16:02:22.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:22.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.363][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-04-04 16:02:22.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-04-04 16:02:22.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.368][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:22.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-04-04 16:02:22.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.373][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:02:22.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:02:22.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.378][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:02:22.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:02:22.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.383][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-04-04 16:02:22.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-04-04 16:02:22.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.393][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-04-04 16:02:22.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-04-04 16:02:22.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.409][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-04-04 16:02:22.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-04-04 16:02:22.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.452][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-04-04 16:02:22.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-04-04 16:02:22.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.457][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-04-04 16:02:22.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-04-04 16:02:22.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.462][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-04-04 16:02:22.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-04-04 16:02:22.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.490][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.491][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.492][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.493][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.510][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:22.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:22.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.515][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:22.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:22.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.520][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:22.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:22.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.525][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:22.527][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:22.528][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.529][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.530][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:22.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:22.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.546][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:22.547][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:22.549][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.550][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:22.556][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:22.557][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:22.559][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:22.560][ef$get] fields variable is a list.
biodb.INFO [2026-04-04 16:02:22.575][biodb::testThat]
biodb.INFO [2026-04-04 16:02:22.576][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-04-04 16:02:22.578][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:22.579][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:22.581][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2026-04-04 16:02:22.586][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2026-04-04 16:02:22.588][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-04-04 16:02:22.590][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:22.591][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:22.592][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:22.593][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-04-04 16:02:22.595][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-04-04 16:02:22.651][biodb::testThat]
biodb.INFO [2026-04-04 16:02:22.653][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-04-04 16:02:22.654][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:22.655][biodb::testThat]
biodb.INFO [2026-04-04 16:02:22.663][biodb::testThat]
biodb.INFO [2026-04-04 16:02:22.664][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-04-04 16:02:22.665][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:22.666][biodb::testThat]
biodb.WARN [2026-04-04 16:02:22.669][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-04-04 16:02:22.673][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-04-04 16:02:22.683][biodb::testThat]
biodb.INFO [2026-04-04 16:02:22.684][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-04-04 16:02:22.686][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:22.687][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:22.692][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2026-04-04 16:02:22.693][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2026-04-04 16:02:22.695][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-04-04 16:02:22.696][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2026-04-04 16:02:22.697][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:22.699][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-04-04 16:02:22.700][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-04-04 16:02:22.701][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-04-04 16:02:22.765][biodb::testThat]
biodb.INFO [2026-04-04 16:02:22.766][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-04-04 16:02:22.767][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:22.768][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-04-04 16:02:22.827][biodb::testThat]
biodb.INFO [2026-04-04 16:02:22.828][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-04-04 16:02:22.829][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:22.830][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-04-04 16:02:22.894][biodb::testThat]
biodb.INFO [2026-04-04 16:02:22.895][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-04-04 16:02:22.896][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:22.898][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-04-04 16:02:22.957][biodb::testThat]
biodb.INFO [2026-04-04 16:02:22.958][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-04-04 16:02:22.960][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:22.961][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-04-04 16:02:23.020][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-04-04 16:02:23.021][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2026-04-04 16:02:23.023][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-04-04 16:02:23.024][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:23.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:23.026][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:23.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:23.029][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:23.036][FUN] Functions in observer 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  8.1Mb
  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)