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"	4873
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"	4654
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CHECK results for biodbNcbi on merida1

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

raw results

Summary

Package: biodbNcbi

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.14.0.tar.gz

StartedAt: 2025-11-22 16:01:58 -0500 (Sat, 22 Nov 2025)

EndedAt: 2025-11-22 16:03:15 -0500 (Sat, 22 Nov 2025)

EllapsedTime: 76.6 seconds

RetCode: 1

Status: ERROR

CheckDir: biodbNcbi.Rcheck

Warnings: NA

Tests output

biodbNcbi.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 Patched (2025-11-05 r88990) -- "[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 [2025-11-22 16:03:02.436][biodb::testContext]
biodb.INFO [2025-11-22 16:03:02.440][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-22 16:03:02.441][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2025-11-22 16:03:02.442][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-22 16:03:02.444][biodb::testContext]
biodb.INFO [2025-11-22 16:03:02.451][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-22 16:03:02.453][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-11-22 16:03:02.461][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:03:02.462][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-22 16:03:02.464][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-22 16:03:02.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.469][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-22 16:03:02.494][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-22 16:03:02.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.508][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-22 16:03:02.509][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-22 16:03:02.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.514][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-22 16:03:02.515][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-22 16:03:02.516][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-22 16:03:02.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.521][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-22 16:03:02.522][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-22 16:03:02.524][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-22 16:03:02.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.528][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-22 16:03:02.530][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-22 16:03:02.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.534][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-22 16:03:02.535][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-22 16:03:02.537][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-22 16:03:02.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.541][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-22 16:03:02.543][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-22 16:03:02.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.547][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-22 16:03:02.548][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-22 16:03:02.550][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-22 16:03:02.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.554][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-22 16:03:02.555][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-22 16:03:02.557][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-22 16:03:02.558][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-22 16:03:02.559][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-22 16:03:02.560][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-22 16:03:02.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.565][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-22 16:03:02.566][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-22 16:03:02.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.571][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-22 16:03:02.572][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-22 16:03:02.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.577][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-22 16:03:02.578][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-22 16:03:02.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.583][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-22 16:03:02.584][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-22 16:03:02.585][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-22 16:03:02.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.590][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-22 16:03:02.591][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-22 16:03:02.601][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-22 16:03:02.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.605][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-22 16:03:02.607][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-22 16:03:02.608][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-22 16:03:02.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.616][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-22 16:03:02.659][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:02.681][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-11-22 16:03:02.682][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:02.683][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:02.685][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:02.686][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:02.687][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:02.689][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:02.690][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-22 16:03:02.691][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:02.692][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:02.694][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-22 16:03:02.695][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:02.696][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:02.697][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:02.699][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:02.699][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:03:02.699][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:03:02.699][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-22 16:03:02.699][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-22 16:03:02.700][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:02.701][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:02.702][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:02.704][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:02.705][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:02.706][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:02.707][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:02.709][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:02.710][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:02.711][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:02.712][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:02.713][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:02.715][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-22 16:03:02.717][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:02.718][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-22 16:03:02.720][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:02.721][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:02.722][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:02.728][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:02.729][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:02.731][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:02.732][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-22 16:03:02.733][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:02.734][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:02.736][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-22 16:03:02.737][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:02.738][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:02.739][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:02.741][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:02.741][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:03:02.741][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:03:02.741][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-22 16:03:02.741][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-22 16:03:02.742][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:02.743][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:02.744][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:02.746][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:02.747][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:02.748][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:02.749][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:02.750][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:02.751][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:02.753][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:02.754][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:02.755][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:02.757][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-22 16:03:02.759][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:02.760][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-11-22 16:03:02.761][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:02.763][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:02.764][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:02.765][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:02.766][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:02.767][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:02.769][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-22 16:03:02.770][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:02.771][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:02.772][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-22 16:03:02.774][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:02.775][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:02.776][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:02.777][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:02.779][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:02.780][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:02.781][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:02.782][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:02.783][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:02.785][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:02.786][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:02.787][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:02.788][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:02.789][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:02.790][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:02.792][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:02.793][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-22 16:03:02.795][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:02.797][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-22 16:03:02.798][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:02.799][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:02.800][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:02.802][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:02.803][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:02.804][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:02.806][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-22 16:03:02.807][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:02.808][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:02.809][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-22 16:03:02.811][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:02.812][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:02.813][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:02.814][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:02.816][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:02.817][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:02.818][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:02.819][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:02.820][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:02.822][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:02.823][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:02.824][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:02.825][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:02.826][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:02.828][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:02.829][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:02.833][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:03:02.834][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.835][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[2025-11-22 16:03:02.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:02.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:02.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.841][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[2025-11-22 16:03:02.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:02.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:02.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:02.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:02.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:02.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:02.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:02.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:02.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:02.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:02.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:02.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:02.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:02.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:02.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:02.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:02.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:02.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:02.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:02.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:02.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:02.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:02.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:02.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:02.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:02.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:02.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:02.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:02.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:02.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:02.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:02.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:02.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:02.928][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-22 16:03:02.932][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-22 16:03:02.934][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-22 16:03:02.936][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-22 16:03:02.943][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-22 16:03:02.945][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-22 16:03:02.947][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-22 16:03:02.949][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-22 16:03:02.950][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-22 16:03:02.952][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-22 16:03:02.954][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-22 16:03:02.955][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-22 16:03:02.957][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-22 16:03:02.959][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-22 16:03:02.961][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-22 16:03:02.962][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-22 16:03:02.964][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-22 16:03:02.966][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-22 16:03:02.968][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-22 16:03:02.970][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-22 16:03:02.972][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-22 16:03:02.974][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-22 16:03:02.975][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-22 16:03:02.977][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-22 16:03:02.979][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-22 16:03:02.981][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-22 16:03:02.983][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-22 16:03:02.985][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-22 16:03:02.986][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-22 16:03:02.988][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-22 16:03:02.990][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-22 16:03:02.992][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-22 16:03:02.993][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-22 16:03:02.995][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-22 16:03:02.997][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-22 16:03:02.998][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-22 16:03:03.000][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-22 16:03:03.002][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-22 16:03:03.004][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-22 16:03:03.006][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-22 16:03:03.007][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-22 16:03:03.009][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-22 16:03:03.011][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-22 16:03:03.012][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-22 16:03:03.014][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-22 16:03:03.016][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-22 16:03:03.018][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-22 16:03:03.019][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-22 16:03:03.021][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-22 16:03:03.023][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-22 16:03:03.024][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-22 16:03:03.026][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-22 16:03:03.028][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-22 16:03:03.029][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-22 16:03:03.031][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-22 16:03:03.033][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-22 16:03:03.035][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-22 16:03:03.036][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-22 16:03:03.038][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-22 16:03:03.040][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-22 16:03:03.041][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-22 16:03:03.043][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-22 16:03:03.045][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-22 16:03:03.047][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-22 16:03:03.048][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-22 16:03:03.050][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-22 16:03:03.052][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-22 16:03:03.053][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-22 16:03:03.055][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-22 16:03:03.057][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-22 16:03:03.059][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-22 16:03:03.060][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-22 16:03:03.062][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-22 16:03:03.064][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-22 16:03:03.066][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-22 16:03:03.067][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-22 16:03:03.069][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-22 16:03:03.071][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-22 16:03:03.073][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-22 16:03:03.074][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-22 16:03:03.076][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-22 16:03:03.078][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-22 16:03:03.080][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-22 16:03:03.087][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-22 16:03:03.089][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-22 16:03:03.092][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:03:03.093][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.096][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:03.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:03.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:03.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:03.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:03.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:03.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:03.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:03.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:03.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:03.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:03.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:03.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:03.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:03.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:03.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:03.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:03.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:03.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:03.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:03.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:03.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:03.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:03.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:03.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:03.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:03.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:03.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:03.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:03.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:03.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:03.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:03.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:03.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:03.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:03.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:03.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.178][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[2025-11-22 16:03:03.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:03.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:03.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:03.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:03.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:03.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:03.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:03.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.194][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[2025-11-22 16:03:03.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:03.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:03.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:03.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:03.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:03.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:03.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:03.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:03.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:03.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:03.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:03.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:03.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:03.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:03.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:03.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:03.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:03.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:03.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:03.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:03.236][bdb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-11-22 16:03:03.249][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-11-22 16:03:03.252][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.253][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-11-22 16:03:03.255][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.256][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:03.257][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.258][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:03.260][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.261][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:03.262][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-11-22 16:03:03.264][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:03.265][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.266][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-11-22 16:03:03.268][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:03.269][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-11-22 16:03:03.269][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-11-22 16:03:03.270][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:03.271][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:03.273][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-22 16:03:03.274][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:03.275][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:03.276][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:03.277][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:03.278][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:03.280][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:03.281][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-11-22 16:03:03.281][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-11-22 16:03:03.282][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:03.283][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:03.284][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.286][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:03.287][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-11-22 16:03:03.290][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.291][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-11-22 16:03:03.292][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.293][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:03.294][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.296][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:03.297][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.298][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:03.299][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-22 16:03:03.301][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:03.302][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.303][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-11-22 16:03:03.304][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:03.306][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-11-22 16:03:03.306][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-11-22 16:03:03.306][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-11-22 16:03:03.306][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-11-22 16:03:03.306][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-11-22 16:03:03.306][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-11-22 16:03:03.307][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:03.308][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:03.309][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-22 16:03:03.311][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:03.312][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:03.313][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:03.314][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:03.315][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:03.316][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:03.318][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:03.318][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-22 16:03:03.319][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:03.320][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:03.321][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.322][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:03.324][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-11-22 16:03:03.326][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:03.328][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-11-22 16:03:03.329][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.330][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:03.331][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.332][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:03.334][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.335][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:03.336][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-22 16:03:03.337][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:03.339][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.340][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-11-22 16:03:03.341][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:03.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-11-22 16:03:03.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:03.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:03.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:03.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:03.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:03.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:03.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:03.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:03.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:03.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-11-22 16:03:03.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:03.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:03.343][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:03.348][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:03.349][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:03.349][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:03:03.349][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:03:03.350][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-11-22 16:03:03.351][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:03.353][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:03.354][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:03.355][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:03.356][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:03.358][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:03.359][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:03.359][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-22 16:03:03.359][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-11-22 16:03:03.360][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:03.361][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:03.362][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.364][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-11-22 16:03:03.365][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-11-22 16:03:03.368][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.369][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-11-22 16:03:03.370][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.371][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:03.372][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.374][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:03.375][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.376][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:03.377][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-22 16:03:03.379][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:03.380][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.381][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-11-22 16:03:03.382][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:03.384][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-11-22 16:03:03.384][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-11-22 16:03:03.385][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:03.386][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:03.387][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-11-22 16:03:03.389][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:03.390][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:03.391][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:03.392][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:03.393][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:03.394][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:03.396][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:03.396][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-22 16:03:03.396][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-11-22 16:03:03.397][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:03.398][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:03.399][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:03.400][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-11-22 16:03:03.408][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-11-22 16:03:03.410][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-22 16:03:03.412][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-22 16:03:03.414][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-11-22 16:03:03.416][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-22 16:03:03.418][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-11-22 16:03:03.440][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-11-22 16:03:03.457][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2025-11-22 16:03:03.467][biodb::testThat]
biodb.INFO [2025-11-22 16:03:03.468][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-22 16:03:03.469][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:03.470][biodb::testThat]
biodb.TRACE[2025-11-22 16:03:03.475][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2025-11-22 16:03:03.477][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-11-22 16:03:03.481][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-11-22 16:03:03.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:03:03.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:03.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:03.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.511][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:03:03.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.554][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-11-22 16:03:03.571][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:03.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.574][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.619][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-11-22 16:03:03.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:03.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.624][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:03.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:03.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.629][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:03.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:03.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.639][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:03.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:03.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:03:03.718][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2025-11-22 16:03:03.721][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-22 16:03:03.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:03.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.726][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-22 16:03:03.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:03.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.803][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:03:03.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:03:03.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.809][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:03:03.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:03:03.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.814][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-22 16:03:03.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-22 16:03:03.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.819][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-22 16:03:03.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-22 16:03:03.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.846][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:03.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:03.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.891][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:03.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:03.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.895][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:03.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:03.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.900][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:03.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:03.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.933][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.935][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.937][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:03.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:03.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.953][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-11-22 16:03:03.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:03.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.958][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-22 16:03:03.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:03.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.963][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-22 16:03:03.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:03.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.969][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-11-22 16:03:03.970][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:03.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.972][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.973][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-11-22 16:03:03.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:03.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.988][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-22 16:03:03.990][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:03.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:03.992][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:03.999][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.000][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.003][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.026][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2025-11-22 16:03:04.074][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-11-22 16:03:04.076][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-11-22 16:03:04.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:03:04.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:04.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:04.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:04.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:04.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:04.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:03:04.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.137][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-11-22 16:03:04.139][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:04.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.141][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.143][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-11-22 16:03:04.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:04.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.148][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:04.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:04.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.153][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:04.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:04.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.163][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:04.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:04.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:03:04.199][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2025-11-22 16:03:04.226][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-22 16:03:04.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:04.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.231][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-22 16:03:04.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:04.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.236][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:03:04.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:03:04.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.241][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:03:04.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:03:04.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.251][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-22 16:03:04.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-22 16:03:04.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.256][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-22 16:03:04.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-22 16:03:04.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.272][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:04.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:04.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.314][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:04.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:04.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.319][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:04.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:04.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.324][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:04.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:04.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.365][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.366][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.369][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.385][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-11-22 16:03:04.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:04.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.390][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-22 16:03:04.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:04.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.395][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-22 16:03:04.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:04.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.400][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-11-22 16:03:04.401][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:04.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.404][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.405][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-11-22 16:03:04.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:04.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.424][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-22 16:03:04.425][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:04.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.428][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:04.434][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:04.436][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:04.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:04.438][ef$get] fields variable is a list.
biodb.INFO [2025-11-22 16:03:04.449][biodb::testThat]
biodb.INFO [2025-11-22 16:03:04.450][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-22 16:03:04.451][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:04.453][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:04.456][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2025-11-22 16:03:04.458][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2025-11-22 16:03:04.462][self$getFolder] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704".
fscache.INFO [2025-11-22 16:03:04.464][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-11-22 16:03:04.465][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:04.467][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-11-22 16:03:04.468][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:04.469][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2025-11-22 16:03:04.647][biodb::testThat]
biodb.INFO [2025-11-22 16:03:04.648][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-22 16:03:04.649][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:04.650][biodb::testThat]
biodb.INFO [2025-11-22 16:03:04.658][biodb::testThat]
biodb.INFO [2025-11-22 16:03:04.659][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-22 16:03:04.661][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:04.662][biodb::testThat]
biodb.WARN [2025-11-22 16:03:04.686][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-11-22 16:03:04.716][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-11-22 16:03:04.727][biodb::testThat]
biodb.INFO [2025-11-22 16:03:04.728][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-22 16:03:04.729][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:04.731][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:04.754][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2025-11-22 16:03:04.818][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-11-22 16:03:04.865][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-11-22 16:03:04.866][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:04.868][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-11-22 16:03:04.869][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:04.870][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2025-11-22 16:03:04.965][biodb::testThat]
biodb.INFO [2025-11-22 16:03:04.966][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-22 16:03:04.968][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:04.969][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2025-11-22 16:03:05.029][biodb::testThat]
biodb.INFO [2025-11-22 16:03:05.030][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-22 16:03:05.032][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:05.033][biodb::testThat]
biodb.INFO [2025-11-22 16:03:05.043][biodb::testThat]
biodb.INFO [2025-11-22 16:03:05.045][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-22 16:03:05.046][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:05.047][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2025-11-22 16:03:05.111][biodb::testThat]
biodb.INFO [2025-11-22 16:03:05.112][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-22 16:03:05.113][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:05.114][biodb::testThat]
biodb.INFO [2025-11-22 16:03:05.123][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-22 16:03:05.124][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-11-22 16:03:05.125][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-22 16:03:05.126][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:05.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:05.129][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.131][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-11-22 16:03:05.145][biodb::testContext]
biodb.INFO [2025-11-22 16:03:05.147][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-22 16:03:05.148][biodb::testContext] Test context - Gene long tests
biodb.INFO [2025-11-22 16:03:05.149][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-22 16:03:05.151][biodb::testContext]
biodb.INFO [2025-11-22 16:03:05.153][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-22 16:03:05.155][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-11-22 16:03:05.160][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:03:05.161][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-22 16:03:05.163][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-22 16:03:05.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.167][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-22 16:03:05.169][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-22 16:03:05.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.173][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-22 16:03:05.175][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-22 16:03:05.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.179][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-22 16:03:05.180][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-22 16:03:05.182][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-22 16:03:05.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.186][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-22 16:03:05.188][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-22 16:03:05.189][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-22 16:03:05.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.193][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-22 16:03:05.195][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-22 16:03:05.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.199][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-22 16:03:05.201][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-22 16:03:05.202][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-22 16:03:05.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.206][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-22 16:03:05.208][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-22 16:03:05.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.212][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-22 16:03:05.214][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-22 16:03:05.215][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-22 16:03:05.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.219][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-22 16:03:05.221][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-22 16:03:05.222][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-22 16:03:05.223][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-22 16:03:05.224][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-22 16:03:05.226][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-22 16:03:05.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.230][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-22 16:03:05.231][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-22 16:03:05.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.236][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-22 16:03:05.237][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-22 16:03:05.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.242][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-22 16:03:05.248][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-22 16:03:05.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.253][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-22 16:03:05.254][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-22 16:03:05.255][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-22 16:03:05.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.260][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-22 16:03:05.261][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-22 16:03:05.271][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-22 16:03:05.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.276][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-22 16:03:05.277][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-22 16:03:05.278][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-22 16:03:05.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.283][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-22 16:03:05.286][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:05.287][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-11-22 16:03:05.288][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.289][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:05.291][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.292][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.293][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:05.294][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.296][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-22 16:03:05.297][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:05.298][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.299][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-22 16:03:05.301][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:05.302][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:05.303][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.304][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:05.304][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:03:05.304][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:03:05.304][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-22 16:03:05.304][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-22 16:03:05.306][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:05.307][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:05.308][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:05.309][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:05.311][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:05.312][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:05.313][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.314][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:05.315][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:05.316][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:05.318][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:05.319][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:05.320][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-22 16:03:05.323][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:05.324][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-22 16:03:05.325][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.326][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:05.328][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.329][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.330][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:05.332][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.333][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-22 16:03:05.334][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:05.335][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.337][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-22 16:03:05.338][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:05.339][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:05.341][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.342][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:05.342][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:03:05.342][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:03:05.342][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-22 16:03:05.342][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-22 16:03:05.343][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:05.345][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:05.346][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:05.347][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:05.348][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:05.349][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:05.351][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.352][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:05.353][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:05.355][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:05.356][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:05.358][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:05.359][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-22 16:03:05.362][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.363][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-11-22 16:03:05.365][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.366][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:05.368][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.369][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.370][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:05.372][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.373][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-22 16:03:05.375][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:05.376][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:05.378][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-22 16:03:05.379][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:05.380][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:05.381][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.383][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:05.384][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:05.385][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:05.386][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:05.388][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:05.389][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:05.390][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:05.391][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.393][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:05.394][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:05.395][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:05.396][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:05.398][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:05.403][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-22 16:03:05.406][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.407][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-22 16:03:05.408][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.409][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:05.411][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.412][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.413][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:05.414][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.415][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-22 16:03:05.417][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:05.418][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:05.419][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-22 16:03:05.421][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:05.422][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:05.423][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.424][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:05.426][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:05.427][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:05.428][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:05.429][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:05.430][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:05.431][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:05.433][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.434][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:05.435][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:05.436][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:05.437][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:05.439][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:05.440][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:03:05.441][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.460][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[2025-11-22 16:03:05.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.536][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-22 16:03:05.537][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-22 16:03:05.539][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-22 16:03:05.545][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-22 16:03:05.547][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-22 16:03:05.548][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-22 16:03:05.550][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-22 16:03:05.552][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-22 16:03:05.553][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-22 16:03:05.555][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-22 16:03:05.557][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-22 16:03:05.558][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-22 16:03:05.560][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-22 16:03:05.562][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-22 16:03:05.564][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-22 16:03:05.565][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-22 16:03:05.567][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-22 16:03:05.569][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-22 16:03:05.570][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-22 16:03:05.572][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-22 16:03:05.574][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-22 16:03:05.576][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-22 16:03:05.577][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-22 16:03:05.579][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-22 16:03:05.581][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-22 16:03:05.583][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-22 16:03:05.584][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-22 16:03:05.586][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-22 16:03:05.588][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-22 16:03:05.589][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-22 16:03:05.591][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-22 16:03:05.593][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-22 16:03:05.595][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-22 16:03:05.596][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-22 16:03:05.598][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-22 16:03:05.600][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-22 16:03:05.601][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-22 16:03:05.603][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-22 16:03:05.605][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-22 16:03:05.607][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-22 16:03:05.608][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-22 16:03:05.610][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-22 16:03:05.612][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-22 16:03:05.614][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-22 16:03:05.615][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-22 16:03:05.617][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-22 16:03:05.619][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-22 16:03:05.621][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-22 16:03:05.622][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-22 16:03:05.624][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-22 16:03:05.626][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-22 16:03:05.628][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-22 16:03:05.629][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-22 16:03:05.631][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-22 16:03:05.633][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-22 16:03:05.635][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-22 16:03:05.636][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-22 16:03:05.638][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-22 16:03:05.640][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-22 16:03:05.642][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-22 16:03:05.643][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-22 16:03:05.645][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-22 16:03:05.647][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-22 16:03:05.649][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-22 16:03:05.650][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-22 16:03:05.652][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-22 16:03:05.654][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-22 16:03:05.656][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-22 16:03:05.657][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-22 16:03:05.659][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-22 16:03:05.661][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-22 16:03:05.663][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-22 16:03:05.664][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-22 16:03:05.666][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-22 16:03:05.668][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-22 16:03:05.670][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-22 16:03:05.672][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-22 16:03:05.673][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-22 16:03:05.675][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-22 16:03:05.677][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-22 16:03:05.683][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-22 16:03:05.684][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-22 16:03:05.686][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-22 16:03:05.688][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-22 16:03:05.690][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-22 16:03:05.691][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:03:05.692][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.694][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:05.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:05.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:05.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:05.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:05.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:05.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:05.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:05.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:05.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:05.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:05.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:05.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.742][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[2025-11-22 16:03:05.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:05.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:05.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:05.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:05.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.757][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[2025-11-22 16:03:05.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:05.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:05.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:05.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:05.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:05.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:05.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.780][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[2025-11-22 16:03:05.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:05.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:05.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:05.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:05.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:05.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:05.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:05.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:05.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:05.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:05.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:05.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:05.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:05.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:05.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:05.825][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-11-22 16:03:05.827][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-11-22 16:03:05.829][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.830][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-11-22 16:03:05.832][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.833][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:05.834][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.835][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.837][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.838][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.839][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-11-22 16:03:05.840][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:05.842][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.843][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-11-22 16:03:05.844][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:05.845][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-11-22 16:03:05.845][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-11-22 16:03:05.847][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:05.848][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:05.849][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-22 16:03:05.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:05.851][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:05.853][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:05.854][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:05.855][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:05.856][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.857][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-11-22 16:03:05.857][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-11-22 16:03:05.859][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:05.860][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:05.861][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.862][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:05.864][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-11-22 16:03:05.866][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.867][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-11-22 16:03:05.868][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.870][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:05.871][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.872][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.873][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.875][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.876][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-22 16:03:05.877][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:05.878][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.880][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-11-22 16:03:05.881][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:05.882][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-11-22 16:03:05.882][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-11-22 16:03:05.882][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-11-22 16:03:05.882][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-11-22 16:03:05.882][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-11-22 16:03:05.882][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-11-22 16:03:05.883][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:05.885][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:05.886][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-22 16:03:05.887][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:05.888][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:05.889][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:05.891][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:05.892][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:05.893][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.894][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:05.894][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-22 16:03:05.895][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:05.896][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:05.898][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.899][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:05.900][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-11-22 16:03:05.903][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:05.904][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-11-22 16:03:05.905][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.907][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:05.908][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.909][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.910][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.911][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.913][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-22 16:03:05.914][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:05.915][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.916][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-11-22 16:03:05.918][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:05.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-11-22 16:03:05.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:05.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:05.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:05.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:05.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:05.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:05.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:05.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:05.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:05.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-11-22 16:03:05.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:05.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:05.919][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:05.920][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:05.922][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:05.922][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:03:05.922][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:03:05.923][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-11-22 16:03:05.924][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:05.925][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:05.926][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:05.928][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:05.929][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:05.930][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.931][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:05.931][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-22 16:03:05.931][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-11-22 16:03:05.932][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:05.933][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:05.935][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.936][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-11-22 16:03:05.938][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-11-22 16:03:05.940][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.941][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-11-22 16:03:05.942][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.944][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:05.945][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.946][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.947][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.949][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.950][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-22 16:03:05.951][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:05.957][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.958][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-11-22 16:03:05.960][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:05.961][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-11-22 16:03:05.961][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-11-22 16:03:05.962][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:05.963][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:05.965][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-11-22 16:03:05.966][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:05.967][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:05.968][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:05.969][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:05.970][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:05.972][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:05.973][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:05.973][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-22 16:03:05.973][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-11-22 16:03:05.974][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:05.975][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:05.976][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:05.978][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-11-22 16:03:05.979][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-11-22 16:03:05.981][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-22 16:03:05.983][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-22 16:03:05.985][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-11-22 16:03:05.987][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-22 16:03:05.988][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-11-22 16:03:05.997][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2025-11-22 16:03:06.044][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2025-11-22 16:03:06.050][biodb::testThat]
biodb.INFO [2025-11-22 16:03:06.051][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-22 16:03:06.052][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:06.054][biodb::testThat]
biodb.TRACE[2025-11-22 16:03:06.060][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2025-11-22 16:03:06.061][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-11-22 16:03:06.065][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-11-22 16:03:06.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:03:06.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:06.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:06.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:06.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:06.078][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:06.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:03:06.094][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:06.095][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:06.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.098][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:06.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:06.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.105][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-22 16:03:06.107][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-22 16:03:06.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.109][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.111][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-22 16:03:06.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-22 16:03:06.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.123][ef$get] Asked field names are: location.
biodb.TRACE[2025-11-22 16:03:06.125][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-11-22 16:03:06.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.128][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.130][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-11-22 16:03:06.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-11-22 16:03:06.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.135][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-11-22 16:03:06.136][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-11-22 16:03:06.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.139][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.142][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-11-22 16:03:06.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-11-22 16:03:06.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.147][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-11-22 16:03:06.149][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:06.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.151][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.153][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-11-22 16:03:06.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:06.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.158][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-11-22 16:03:06.160][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-11-22 16:03:06.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.162][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.165][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-11-22 16:03:06.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-11-22 16:03:06.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.174][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:06.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:06.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.180][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-11-22 16:03:06.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-11-22 16:03:06.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.185][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-11-22 16:03:06.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-11-22 16:03:06.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:06.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:06.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.195][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-11-22 16:03:06.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-11-22 16:03:06.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:06.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:06.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:06.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:06.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:06.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:06.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:06.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:06.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:06.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:06.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:06.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:06.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:03:06.230][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2025-11-22 16:03:06.232][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-22 16:03:06.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:06.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.237][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-22 16:03:06.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:06.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.242][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:06.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:06.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.247][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:06.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:06.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:06.252][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:06.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:06.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:03:06.262][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-11-22 16:03:06.302][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-11-22 16:03:06.323][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2025-11-22 16:03:06.324][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2025-11-22 16:03:06.327][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-11-22 16:03:06.330][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-11-22 16:03:06.331][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:06.333][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-11-22 16:03:06.334][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:06.335][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-11-22 16:03:06.400][biodb::testThat]
biodb.INFO [2025-11-22 16:03:06.401][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-22 16:03:06.403][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:06.404][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:06.407][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2025-11-22 16:03:06.408][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2025-11-22 16:03:06.410][self$getFolder] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8".
fscache.INFO [2025-11-22 16:03:06.412][cch$loadContents] Load 8 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-11-22 16:03:06.413][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:06.415][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:06.416][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:06.417][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-22 16:03:06.418][private$retrieveContents] Get entry content(s) for 8 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-11-22 16:03:06.481][biodb::testThat]
biodb.INFO [2025-11-22 16:03:06.482][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-22 16:03:06.483][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:06.485][biodb::testThat]
biodb.TRACE[2025-11-22 16:03:06.489][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:06.490][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:06.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:06.492][ef$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:03:06.494][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2025-11-22 16:03:06.515][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-11-22 16:03:06.516][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-11-22 16:03:06.518][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-11-22 16:03:06.521][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:06.523][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:06.525][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:06.527][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-22 16:03:06.552][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-11-22 16:03:06.640][biodb::testThat]
biodb.INFO [2025-11-22 16:03:06.641][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-22 16:03:06.643][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:06.644][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:06.654][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-11-22 16:03:06.655][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-11-22 16:03:06.657][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-11-22 16:03:06.658][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:06.660][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:06.661][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:06.662][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-22 16:03:06.664][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-11-22 16:03:06.724][biodb::testThat]
biodb.INFO [2025-11-22 16:03:06.725][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-22 16:03:06.727][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:06.728][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:06.733][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-11-22 16:03:06.735][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-11-22 16:03:06.737][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-11-22 16:03:06.738][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:06.739][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:06.741][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:06.742][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-22 16:03:06.743][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-11-22 16:03:06.827][biodb::testThat]
biodb.INFO [2025-11-22 16:03:06.828][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-22 16:03:06.830][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:06.831][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-11-22 16:03:06.894][biodb::testThat]
biodb.INFO [2025-11-22 16:03:06.896][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-22 16:03:06.897][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:06.898][biodb::testThat]
biodb.INFO [2025-11-22 16:03:06.908][biodb::testThat]
biodb.INFO [2025-11-22 16:03:06.910][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-22 16:03:06.911][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:06.912][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-11-22 16:03:06.972][biodb::testThat]
biodb.INFO [2025-11-22 16:03:06.974][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-22 16:03:06.975][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:06.976][biodb::testThat]
biodb.INFO [2025-11-22 16:03:06.985][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-22 16:03:06.986][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2025-11-22 16:03:06.987][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-11-22 16:03:06.989][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-22 16:03:06.990][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:06.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:06.992][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:06.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:06.994][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:06.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-11-22 16:03:07.000][biodb::testContext]
biodb.INFO [2025-11-22 16:03:07.002][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-22 16:03:07.003][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2025-11-22 16:03:07.004][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-22 16:03:07.005][biodb::testContext]
biodb.INFO [2025-11-22 16:03:07.008][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-22 16:03:07.010][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-11-22 16:03:07.014][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:03:07.015][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-22 16:03:07.017][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-22 16:03:07.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.022][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-22 16:03:07.023][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-22 16:03:07.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.033][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-22 16:03:07.035][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-22 16:03:07.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.040][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-22 16:03:07.041][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-22 16:03:07.042][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-22 16:03:07.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.047][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-22 16:03:07.048][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-22 16:03:07.049][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-22 16:03:07.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.054][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-22 16:03:07.056][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-22 16:03:07.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.060][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-22 16:03:07.062][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-22 16:03:07.064][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-22 16:03:07.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.072][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-22 16:03:07.077][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-22 16:03:07.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.085][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-22 16:03:07.088][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-22 16:03:07.090][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-22 16:03:07.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.099][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-22 16:03:07.102][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-22 16:03:07.104][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-22 16:03:07.107][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-22 16:03:07.110][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-22 16:03:07.113][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-22 16:03:07.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.122][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-22 16:03:07.125][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-22 16:03:07.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.134][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-22 16:03:07.137][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-22 16:03:07.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.146][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-22 16:03:07.149][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-22 16:03:07.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.157][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-22 16:03:07.159][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-22 16:03:07.161][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-22 16:03:07.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.169][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-22 16:03:07.172][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-22 16:03:07.189][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-22 16:03:07.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.198][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-22 16:03:07.201][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-22 16:03:07.203][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-22 16:03:07.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.211][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-22 16:03:07.214][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:07.216][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-11-22 16:03:07.217][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.219][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:07.220][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.222][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.223][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:07.224][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.225][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-22 16:03:07.227][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:07.228][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.231][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-22 16:03:07.233][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:07.236][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:07.238][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.240][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:07.240][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:03:07.240][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:03:07.240][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-22 16:03:07.240][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-22 16:03:07.241][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:07.243][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:07.244][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:07.245][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:07.251][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:07.252][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:07.254][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.255][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:07.257][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:07.258][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:07.259][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:07.260][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:07.262][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-22 16:03:07.264][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:07.265][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-22 16:03:07.267][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.268][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:07.269][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.270][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.272][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:07.273][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.274][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-22 16:03:07.276][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:07.277][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.278][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-22 16:03:07.279][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:07.281][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:07.282][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.283][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:07.283][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:03:07.283][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:03:07.283][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-22 16:03:07.283][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-22 16:03:07.285][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:07.286][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:07.287][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:07.288][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:07.290][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:07.291][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:07.292][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.294][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:07.295][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:07.296][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:07.298][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:07.299][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:07.301][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-22 16:03:07.303][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.305][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-11-22 16:03:07.306][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.307][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:07.309][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.310][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.311][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:07.312][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.314][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-22 16:03:07.315][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:07.316][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:07.318][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-22 16:03:07.319][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:07.320][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:07.321][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.323][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:07.324][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:07.325][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:07.326][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:07.328][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:07.329][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:07.330][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:07.331][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.333][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:07.334][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:07.335][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:07.336][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:07.338][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:07.339][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-22 16:03:07.341][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.343][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-22 16:03:07.344][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.345][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:07.347][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.348][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.349][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:07.350][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.352][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-22 16:03:07.353][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:07.354][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:07.356][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-22 16:03:07.357][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:07.358][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:07.360][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.361][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:07.362][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:07.363][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:07.365][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:07.366][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:07.367][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:07.368][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:07.370][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.371][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:07.372][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:07.374][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:07.375][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:07.376][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:07.378][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:03:07.379][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.391][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[2025-11-22 16:03:07.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.414][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[2025-11-22 16:03:07.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.420][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[2025-11-22 16:03:07.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.476][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[2025-11-22 16:03:07.477][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-22 16:03:07.479][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-22 16:03:07.481][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-22 16:03:07.482][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-22 16:03:07.484][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-22 16:03:07.486][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-22 16:03:07.488][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-22 16:03:07.489][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-22 16:03:07.491][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-22 16:03:07.493][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-22 16:03:07.494][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-22 16:03:07.496][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-22 16:03:07.498][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-22 16:03:07.500][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-22 16:03:07.501][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-22 16:03:07.503][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-22 16:03:07.505][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-22 16:03:07.506][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-22 16:03:07.508][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-22 16:03:07.510][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-22 16:03:07.512][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-22 16:03:07.513][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-22 16:03:07.520][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-22 16:03:07.522][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-22 16:03:07.523][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-22 16:03:07.525][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-22 16:03:07.527][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-22 16:03:07.529][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-22 16:03:07.530][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-22 16:03:07.532][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-22 16:03:07.534][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-22 16:03:07.536][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-22 16:03:07.537][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-22 16:03:07.539][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-22 16:03:07.541][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-22 16:03:07.543][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-22 16:03:07.545][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-22 16:03:07.546][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-22 16:03:07.548][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-22 16:03:07.550][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-22 16:03:07.551][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-22 16:03:07.553][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-22 16:03:07.555][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-22 16:03:07.557][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-22 16:03:07.558][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-22 16:03:07.560][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-22 16:03:07.562][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-22 16:03:07.564][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-22 16:03:07.565][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-22 16:03:07.567][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-22 16:03:07.569][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-22 16:03:07.570][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-22 16:03:07.572][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-22 16:03:07.574][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-22 16:03:07.576][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-22 16:03:07.577][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-22 16:03:07.579][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-22 16:03:07.581][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-22 16:03:07.583][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-22 16:03:07.584][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-22 16:03:07.586][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-22 16:03:07.588][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-22 16:03:07.589][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-22 16:03:07.591][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-22 16:03:07.593][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-22 16:03:07.595][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-22 16:03:07.596][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-22 16:03:07.598][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-22 16:03:07.600][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-22 16:03:07.602][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-22 16:03:07.603][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-22 16:03:07.605][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-22 16:03:07.607][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-22 16:03:07.608][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-22 16:03:07.610][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-22 16:03:07.612][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-22 16:03:07.614][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-22 16:03:07.615][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-22 16:03:07.617][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-22 16:03:07.619][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-22 16:03:07.621][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-22 16:03:07.622][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-22 16:03:07.624][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-22 16:03:07.626][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-22 16:03:07.628][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-22 16:03:07.629][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:03:07.630][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.632][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:07.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:07.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:07.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:07.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.654][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[2025-11-22 16:03:07.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:07.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:07.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:07.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:07.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:07.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:07.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.678][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[2025-11-22 16:03:07.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:07.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:07.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:07.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:07.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:07.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:07.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:07.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:07.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:07.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:07.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:07.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:07.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:07.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:07.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.740][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[2025-11-22 16:03:07.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:07.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:07.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:07.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:07.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.769][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[2025-11-22 16:03:07.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:07.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:07.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:07.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:07.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:07.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:07.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:07.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:07.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:07.797][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-11-22 16:03:07.800][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-11-22 16:03:07.810][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.812][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-11-22 16:03:07.814][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.815][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:07.816][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.818][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.819][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.820][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.821][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-11-22 16:03:07.822][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:07.824][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.825][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-11-22 16:03:07.826][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:07.828][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-11-22 16:03:07.828][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-11-22 16:03:07.829][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:07.830][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:07.831][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-22 16:03:07.833][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:07.834][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:07.835][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:07.836][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:07.837][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:07.838][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.839][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-11-22 16:03:07.839][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-11-22 16:03:07.841][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:07.843][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:07.845][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.847][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:07.850][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-11-22 16:03:07.853][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.855][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-11-22 16:03:07.856][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.857][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:07.858][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.859][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.861][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.862][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.863][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-22 16:03:07.864][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:07.866][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.867][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-11-22 16:03:07.868][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:07.869][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-11-22 16:03:07.869][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-11-22 16:03:07.869][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-11-22 16:03:07.869][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-11-22 16:03:07.869][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-11-22 16:03:07.869][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-11-22 16:03:07.871][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:07.872][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:07.873][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-22 16:03:07.874][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:07.876][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:07.877][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:07.878][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:07.879][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:07.880][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.881][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:07.881][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-22 16:03:07.883][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:07.884][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:07.885][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.886][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:07.888][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-11-22 16:03:07.890][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:07.892][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-11-22 16:03:07.893][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.894][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:07.895][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.897][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.898][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.899][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.900][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-22 16:03:07.902][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:07.903][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.904][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-11-22 16:03:07.905][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:07.907][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-11-22 16:03:07.907][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:07.907][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:07.907][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:07.907][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:07.907][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:07.907][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:07.907][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:07.907][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:07.907][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:07.907][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-11-22 16:03:07.907][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:07.907][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:07.907][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:07.908][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:07.909][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:07.909][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:03:07.909][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:03:07.911][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-11-22 16:03:07.912][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:07.913][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:07.914][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:07.916][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:07.917][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:07.919][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.920][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:07.920][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-22 16:03:07.920][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-11-22 16:03:07.922][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:07.923][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:07.925][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.927][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-11-22 16:03:07.930][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-11-22 16:03:07.934][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.938][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-11-22 16:03:07.940][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.942][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:07.945][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.947][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.949][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.952][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.954][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-22 16:03:07.956][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:07.966][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:07.969][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-11-22 16:03:07.971][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:07.974][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-11-22 16:03:07.974][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-11-22 16:03:07.976][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:07.979][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:07.981][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-11-22 16:03:07.983][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:07.985][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:07.988][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:07.990][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:07.992][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:07.994][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:07.996][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:07.996][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-22 16:03:07.996][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-11-22 16:03:07.999][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:08.001][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:08.003][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:08.006][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-11-22 16:03:08.009][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-11-22 16:03:08.013][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-22 16:03:08.017][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-22 16:03:08.020][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-11-22 16:03:08.023][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-22 16:03:08.026][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-11-22 16:03:08.043][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2025-11-22 16:03:08.059][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2025-11-22 16:03:08.068][biodb::testThat]
biodb.INFO [2025-11-22 16:03:08.070][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-22 16:03:08.073][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:08.075][biodb::testThat]
biodb.TRACE[2025-11-22 16:03:08.081][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2025-11-22 16:03:08.083][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-11-22 16:03:08.090][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-11-22 16:03:08.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:03:08.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:08.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:08.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:08.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:08.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:08.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:03:08.125][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.128][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.132][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.145][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.147][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.152][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.155][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.165][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.167][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.172][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.175][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.184][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.187][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.192][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.195][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.206][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:08.209][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:08.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.223][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.226][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:08.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:08.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.233][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.235][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.237][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.239][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.244][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-11-22 16:03:08.246][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:08.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.248][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.250][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-11-22 16:03:08.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:08.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.255][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:08.256][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:08.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.258][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.260][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:08.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:08.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.265][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:08.267][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:08.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.269][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:08.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:08.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.276][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:08.277][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:08.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.279][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.281][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:08.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:08.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.286][ef$get] Asked field names are: logp.
biodb.TRACE[2025-11-22 16:03:08.287][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-22 16:03:08.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.290][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.291][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-22 16:03:08.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-22 16:03:08.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.296][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-11-22 16:03:08.298][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:08.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.300][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-11-22 16:03:08.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:08.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.307][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:08.308][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:08.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.310][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.312][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:08.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:08.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.317][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:08.318][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:08.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.321][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.322][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:08.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:08.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.327][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-11-22 16:03:08.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.332][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.337][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.342][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-11-22 16:03:08.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.352][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.357][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.362][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-11-22 16:03:08.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.366][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.371][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.376][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-11-22 16:03:08.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:08.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.381][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:08.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:08.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.386][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:08.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:08.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.391][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-11-22 16:03:08.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.396][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.401][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.406][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:08.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:08.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.411][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:08.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:08.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.416][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:08.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:08.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.426][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:08.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:08.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:03:08.461][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2025-11-22 16:03:08.464][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-22 16:03:08.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:08.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.473][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-22 16:03:08.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:08.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.478][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:08.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:08.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.483][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:03:08.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:03:08.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.488][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:03:08.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:03:08.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.493][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-22 16:03:08.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-22 16:03:08.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.498][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-22 16:03:08.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-22 16:03:08.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.515][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:08.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:08.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.558][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:08.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:08.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.563][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:08.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:08.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.568][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:08.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:08.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.601][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.602][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.604][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:08.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:08.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.621][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-11-22 16:03:08.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:08.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:08.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:08.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:08.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:08.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.637][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-11-22 16:03:08.639][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:08.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.641][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.642][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-11-22 16:03:08.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:08.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-11-22 16:03:08.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:08.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:08.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:08.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:08.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:08.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.673][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-11-22 16:03:08.675][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:08.676][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.677][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.679][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-11-22 16:03:08.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:08.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.694][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:08.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:08.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.700][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:08.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:08.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.706][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:08.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:08.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.711][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:08.713][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:08.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.715][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.716][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:08.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:08.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.737][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-22 16:03:08.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-22 16:03:08.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.742][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-22 16:03:08.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-22 16:03:08.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.747][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-22 16:03:08.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-22 16:03:08.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.752][ef$get] Asked field names are: logp.
biodb.TRACE[2025-11-22 16:03:08.754][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-22 16:03:08.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.756][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.757][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-22 16:03:08.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-22 16:03:08.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.773][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:08.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:08.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.778][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:08.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:08.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.783][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:08.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:08.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.788][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:08.789][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:08.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.792][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.793][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:08.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:08.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.808][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:08.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:08.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.814][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:08.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:08.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.819][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:08.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:08.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.824][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:08.826][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:08.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.828][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.829][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:08.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:08.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.845][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.855][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.860][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.866][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.867][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.870][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.871][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:08.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.887][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.892][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.898][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.903][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.905][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.906][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.907][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.908][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:08.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.925][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.931][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.936][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.941][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.943][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.945][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.946][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:08.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.962][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.967][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.972][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.977][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.983][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.985][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:08.987][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:08.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:08.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.002][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.007][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.012][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.017][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.018][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.021][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.022][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.037][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:09.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:09.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:09.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:09.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.047][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:09.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:09.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.052][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:09.054][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:09.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.056][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.057][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:09.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:09.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.073][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:09.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:09.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.078][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:09.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:09.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.083][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:09.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:09.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.088][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:09.089][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:09.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.092][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:09.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:09.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.113][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:09.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:09.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.118][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:09.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:09.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:09.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:09.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.127][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:09.129][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:09.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.131][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.132][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:09.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:09.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.147][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.149][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.151][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.157][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:09.159][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:09.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.161][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.167][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:09.169][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:09.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.171][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.177][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:09.179][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:09.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.181][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.187][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.189][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.191][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.198][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:09.199][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:09.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.201][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.207][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:09.209][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:09.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.211][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.217][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:09.219][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:09.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.221][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.227][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:09.229][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:09.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.236][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.242][ef$get] Asked field names are: logp.
biodb.TRACE[2025-11-22 16:03:09.244][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-22 16:03:09.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.246][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.253][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:09.254][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:09.256][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.257][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.263][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:09.265][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:09.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.267][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.273][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:09.275][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:09.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.277][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.284][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:09.285][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:09.286][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.288][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.294][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:09.296][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:09.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.298][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.305][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2025-11-22 16:03:09.307][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-11-22 16:03:09.308][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-11-22 16:03:09.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:03:09.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:09.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:09.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:09.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:09.321][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:09.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:03:09.325][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.327][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.329][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.336][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:09.337][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:09.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.339][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.341][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:09.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:09.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.346][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:09.348][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:09.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.350][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.352][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:09.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:09.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.357][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:09.358][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:09.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.360][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.362][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:09.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:09.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.372][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.373][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.375][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.377][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.382][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:09.383][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:09.385][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.386][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.388][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:09.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:09.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.393][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-11-22 16:03:09.394][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:09.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.397][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.398][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-11-22 16:03:09.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:09.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.403][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:09.405][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:09.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.407][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.409][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:09.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:09.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.414][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:09.415][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:09.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.417][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.419][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:09.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:09.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.424][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:09.425][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:09.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.427][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.429][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:09.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:09.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.434][ef$get] Asked field names are: logp.
biodb.TRACE[2025-11-22 16:03:09.435][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-22 16:03:09.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.438][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.439][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-22 16:03:09.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-22 16:03:09.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.444][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-11-22 16:03:09.446][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:09.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.448][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-11-22 16:03:09.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:09.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.455][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:09.456][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:09.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.458][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.460][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:09.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:09.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.465][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:09.466][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:09.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.468][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.470][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:09.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:09.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.475][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-11-22 16:03:09.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:09.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.480][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:09.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:09.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.489][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:09.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:09.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.494][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-11-22 16:03:09.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:09.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.499][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:09.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:09.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.504][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:09.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:09.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.509][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-11-22 16:03:09.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:09.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.514][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:09.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:09.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.519][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:09.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:09.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.524][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-11-22 16:03:09.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.529][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.534][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:09.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.539][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-11-22 16:03:09.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:09.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.544][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:09.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:09.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.549][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:09.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:09.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.554][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:09.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:09.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.559][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:09.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:09.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.564][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:09.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:09.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.574][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:09.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:09.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:03:09.614][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2025-11-22 16:03:09.616][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-22 16:03:09.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:09.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.621][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-22 16:03:09.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:09.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.626][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:09.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:09.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.631][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:03:09.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:03:09.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.636][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:03:09.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:03:09.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.641][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-22 16:03:09.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-22 16:03:09.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.646][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-22 16:03:09.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-22 16:03:09.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.663][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:09.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:09.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.706][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:09.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:09.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.712][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:09.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:09.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.717][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:09.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:09.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.757][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.758][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.760][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:09.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:09.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:09.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:09.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:09.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:09.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:09.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:09.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.792][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:09.794][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:09.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.796][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:09.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:09.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:09.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:09.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:09.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:09.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:09.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:09.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.828][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:09.829][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:09.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.832][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:09.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:09.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.848][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:09.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:09.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.853][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:09.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:09.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.858][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:09.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:09.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.868][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:09.870][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:09.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.872][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.874][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:09.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:09.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.889][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-22 16:03:09.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-22 16:03:09.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.894][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-22 16:03:09.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-22 16:03:09.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.900][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-22 16:03:09.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-22 16:03:09.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.905][ef$get] Asked field names are: logp.
biodb.TRACE[2025-11-22 16:03:09.906][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-22 16:03:09.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.909][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.910][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-22 16:03:09.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-22 16:03:09.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.926][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:09.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:09.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.932][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:09.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:09.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.937][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:09.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:09.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.942][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:09.944][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:09.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.946][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.947][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:09.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:09.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.964][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:09.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:09.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.970][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:09.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:09.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.975][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:09.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:09.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.980][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:09.981][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:09.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.984][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:09.985][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:09.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:09.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:09.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.006][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:10.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:10.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.011][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:10.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:10.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.016][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:10.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:10.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.022][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:10.023][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:10.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.026][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.027][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:10.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:10.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.042][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:10.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:10.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.048][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:10.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:10.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.053][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:10.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:10.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.059][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:10.060][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:10.061][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.062][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.064][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:10.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:10.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.080][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:10.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:10.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.085][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:10.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:10.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.090][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:10.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:10.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.096][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:10.097][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:10.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.100][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.101][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:10.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:10.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.117][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:10.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:10.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.123][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:10.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:10.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.134][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:10.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:10.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.141][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:10.143][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:10.144][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.145][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.147][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:10.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:10.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.164][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:10.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:10.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.172][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:10.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:10.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.178][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:10.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:10.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.185][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:10.187][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:10.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.190][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.191][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:10.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:10.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.208][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:10.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:10.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.214][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:10.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:10.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.220][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:10.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:10.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.226][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:10.227][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:10.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.230][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.232][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:10.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:10.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.247][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:10.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:10.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.253][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:10.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:10.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.258][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:10.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:10.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.263][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:10.265][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:10.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.267][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.268][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:10.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:10.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.289][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:10.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:10.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.294][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:10.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:10.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.299][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:10.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:10.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.305][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:10.306][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:10.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.308][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.310][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:10.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:10.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.325][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:10.327][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:10.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.329][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.336][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:10.337][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-22 16:03:10.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.340][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.347][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:10.348][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-22 16:03:10.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.351][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.357][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:10.359][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-22 16:03:10.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.361][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.368][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:10.369][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:03:10.371][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.372][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.378][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:10.380][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:03:10.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.382][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.389][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:10.390][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:10.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.393][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.399][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:10.401][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:10.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.404][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.415][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:10.417][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:10.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.420][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.427][ef$get] Asked field names are: logp.
biodb.TRACE[2025-11-22 16:03:10.428][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-22 16:03:10.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.431][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.438][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:10.439][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:10.440][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.441][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.448][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:10.449][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:10.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.452][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.458][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:10.459][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:10.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.462][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.468][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:10.470][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-22 16:03:10.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.472][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:10.478][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:10.480][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-22 16:03:10.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.482][ef$get] fields variable is a list.
biodb.INFO [2025-11-22 16:03:10.492][biodb::testThat]
biodb.INFO [2025-11-22 16:03:10.493][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-22 16:03:10.494][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:10.496][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:10.499][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-11-22 16:03:10.501][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-11-22 16:03:10.503][self$getFolder] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75".
fscache.INFO [2025-11-22 16:03:10.504][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-22 16:03:10.506][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:10.507][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:10.509][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:10.510][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-22 16:03:10.511][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-11-22 16:03:10.574][biodb::testThat]
biodb.INFO [2025-11-22 16:03:10.575][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-22 16:03:10.576][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:10.577][biodb::testThat]
biodb.TRACE[2025-11-22 16:03:10.581][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:10.583][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:10.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:10.585][ef$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:03:10.587][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2025-11-22 16:03:10.598][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-11-22 16:03:10.600][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-11-22 16:03:10.601][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-22 16:03:10.603][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:10.604][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:10.605][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:10.607][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-22 16:03:10.608][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-11-22 16:03:10.672][biodb::testThat]
biodb.INFO [2025-11-22 16:03:10.673][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-22 16:03:10.675][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:10.676][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:10.686][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-11-22 16:03:10.687][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-11-22 16:03:10.689][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-22 16:03:10.691][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:10.692][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:10.693][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:10.695][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-22 16:03:10.696][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-11-22 16:03:10.754][biodb::testThat]
biodb.INFO [2025-11-22 16:03:10.755][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-22 16:03:10.756][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:10.757][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:10.762][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-11-22 16:03:10.764][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-11-22 16:03:10.765][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-22 16:03:10.767][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:10.768][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:10.774][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:10.775][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-22 16:03:10.777][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-11-22 16:03:10.836][biodb::testThat]
biodb.INFO [2025-11-22 16:03:10.837][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-22 16:03:10.838][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:10.839][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-11-22 16:03:10.903][biodb::testThat]
biodb.INFO [2025-11-22 16:03:10.905][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-22 16:03:10.906][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:10.907][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-11-22 16:03:10.965][biodb::testThat]
biodb.INFO [2025-11-22 16:03:10.967][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-22 16:03:10.968][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:10.969][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-11-22 16:03:11.032][biodb::testThat]
biodb.INFO [2025-11-22 16:03:11.034][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-22 16:03:11.035][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:11.036][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2025-11-22 16:03:11.109][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:11.110][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:11.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:11.113][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:11.114][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:11.116][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:11.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:11.118][ef$get] fields variable is a list.
biodb.INFO [2025-11-22 16:03:11.120][biodb::testThat]
biodb.INFO [2025-11-22 16:03:11.121][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-11-22 16:03:11.122][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:11.124][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:11.133][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-11-22 16:03:11.134][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-11-22 16:03:11.136][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-22 16:03:11.137][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:11.138][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:11.140][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:11.141][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-22 16:03:11.142][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-11-22 16:03:11.200][biodb::testThat]
biodb.INFO [2025-11-22 16:03:11.201][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-11-22 16:03:11.202][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:11.208][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:11.213][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-11-22 16:03:11.214][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-11-22 16:03:11.216][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-22 16:03:11.217][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:11.219][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:11.220][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:11.221][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-22 16:03:11.222][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-11-22 16:03:11.280][biodb::testThat]
biodb.INFO [2025-11-22 16:03:11.282][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-11-22 16:03:11.283][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:11.284][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:11.288][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-11-22 16:03:11.289][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-11-22 16:03:11.291][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-22 16:03:11.292][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:11.293][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:11.295][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:11.296][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-22 16:03:11.297][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-11-22 16:03:11.359][biodb::testThat]
biodb.INFO [2025-11-22 16:03:11.361][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-11-22 16:03:11.362][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:11.363][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:11.367][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-11-22 16:03:11.368][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-11-22 16:03:11.370][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-22 16:03:11.371][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:11.373][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:11.374][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:11.375][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-22 16:03:11.377][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2025-11-22 16:03:11.440][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:11.441][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:11.443][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:11.444][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:11.445][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:11.446][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:11.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:11.449][ef$get] fields variable is a list.
biodb.INFO [2025-11-22 16:03:11.451][biodb::testThat]
biodb.INFO [2025-11-22 16:03:11.452][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2025-11-22 16:03:11.453][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:11.454][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:11.458][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-11-22 16:03:11.460][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-11-22 16:03:11.461][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-22 16:03:11.463][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:11.464][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:11.465][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:11.467][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-22 16:03:11.468][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-11-22 16:03:11.528][biodb::testThat]
biodb.INFO [2025-11-22 16:03:11.529][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2025-11-22 16:03:11.535][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:11.536][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:11.540][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-11-22 16:03:11.542][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-11-22 16:03:11.543][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-22 16:03:11.545][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:11.546][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:11.547][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:11.548][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-22 16:03:11.550][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-11-22 16:03:11.609][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-22 16:03:11.610][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2025-11-22 16:03:11.612][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-22 16:03:11.613][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:11.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:11.615][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:11.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:11.617][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-11-22 16:03:11.624][biodb::testContext]
biodb.INFO [2025-11-22 16:03:11.625][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-22 16:03:11.626][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2025-11-22 16:03:11.628][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-22 16:03:11.629][biodb::testContext]
biodb.INFO [2025-11-22 16:03:11.631][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-22 16:03:11.633][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-11-22 16:03:11.638][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:03:11.639][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-22 16:03:11.640][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-22 16:03:11.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.650][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-22 16:03:11.652][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-22 16:03:11.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.657][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-22 16:03:11.658][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-22 16:03:11.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.663][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-22 16:03:11.664][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-22 16:03:11.665][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-22 16:03:11.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.670][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-22 16:03:11.671][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-22 16:03:11.672][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-22 16:03:11.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.677][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-22 16:03:11.678][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-22 16:03:11.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.683][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-22 16:03:11.684][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-22 16:03:11.686][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-22 16:03:11.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.690][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-22 16:03:11.692][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-22 16:03:11.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.696][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-22 16:03:11.698][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-22 16:03:11.699][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-22 16:03:11.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.704][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-22 16:03:11.705][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-22 16:03:11.706][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-22 16:03:11.708][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-22 16:03:11.709][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-22 16:03:11.710][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-22 16:03:11.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.715][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-22 16:03:11.716][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-22 16:03:11.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.721][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-22 16:03:11.722][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-22 16:03:11.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.725][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[2025-11-22 16:03:11.727][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-22 16:03:11.728][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-22 16:03:11.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.733][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-22 16:03:11.734][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-22 16:03:11.735][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-22 16:03:11.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.740][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-22 16:03:11.741][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-22 16:03:11.752][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-22 16:03:11.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.757][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-22 16:03:11.758][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-22 16:03:11.759][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-22 16:03:11.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.764][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-22 16:03:11.767][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:11.768][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-11-22 16:03:11.769][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:11.775][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:11.777][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:11.778][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:11.780][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:11.781][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:11.783][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-22 16:03:11.784][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:11.785][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:11.787][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-22 16:03:11.788][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:11.789][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:11.790][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:11.792][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:11.792][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:03:11.792][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:03:11.792][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-22 16:03:11.792][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-22 16:03:11.793][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:11.794][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:11.795][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:11.796][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:11.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:11.799][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:11.800][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:11.801][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:11.802][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:11.804][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:11.805][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:11.806][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:11.808][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-22 16:03:11.810][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:11.811][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-22 16:03:11.812][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:11.814][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:11.815][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:11.816][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:11.817][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:11.819][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:11.820][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-22 16:03:11.821][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:11.822][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:11.824][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-22 16:03:11.825][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:11.826][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:11.827][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:11.829][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:11.829][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:03:11.829][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:03:11.829][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-22 16:03:11.829][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-22 16:03:11.830][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:11.831][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:11.832][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:11.834][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:11.835][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:11.836][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:11.837][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:11.838][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:11.840][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:11.841][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:11.842][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:11.843][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:11.845][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-22 16:03:11.847][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:11.848][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-11-22 16:03:11.849][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:11.851][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:11.852][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:11.853][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:11.855][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:11.856][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:11.857][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-22 16:03:11.858][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:11.860][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:11.861][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-22 16:03:11.862][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:11.863][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:11.865][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:11.866][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:11.867][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:11.868][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:11.869][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:11.871][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:11.872][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:11.873][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:11.874][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:11.875][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:11.877][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:11.878][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:11.879][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:11.880][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:11.882][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-22 16:03:11.884][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:11.885][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-22 16:03:11.891][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:11.893][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:11.894][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:11.896][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:11.897][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:11.898][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:11.900][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-22 16:03:11.901][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:11.902][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:11.904][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-22 16:03:11.905][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:11.906][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:11.907][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:11.909][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:11.910][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:11.911][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:11.912][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:11.914][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:11.915][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:11.916][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:11.917][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:11.918][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:11.920][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:11.921][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:11.922][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:11.923][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:11.925][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:03:11.926][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:11.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:11.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:11.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:11.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:11.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:11.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:11.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:11.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:11.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:11.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:11.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:11.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:11.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:11.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:11.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:11.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:11.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:11.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:11.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:11.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.984][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[2025-11-22 16:03:11.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:11.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:11.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:11.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:11.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:11.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:11.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:11.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:11.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:11.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:12.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:12.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:12.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:12.152][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-22 16:03:12.154][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-22 16:03:12.156][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-22 16:03:12.157][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-22 16:03:12.159][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-22 16:03:12.161][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-22 16:03:12.162][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-22 16:03:12.164][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-22 16:03:12.165][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-22 16:03:12.167][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-22 16:03:12.169][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-22 16:03:12.170][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-22 16:03:12.172][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-22 16:03:12.174][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-22 16:03:12.175][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-22 16:03:12.177][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-22 16:03:12.179][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-22 16:03:12.180][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-22 16:03:12.182][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-22 16:03:12.184][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-22 16:03:12.185][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-22 16:03:12.187][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-22 16:03:12.189][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-22 16:03:12.191][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-22 16:03:12.192][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-22 16:03:12.194][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-22 16:03:12.196][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-22 16:03:12.197][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-22 16:03:12.199][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-22 16:03:12.201][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-22 16:03:12.202][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-22 16:03:12.204][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-22 16:03:12.206][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-22 16:03:12.207][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-22 16:03:12.209][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-22 16:03:12.211][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-22 16:03:12.212][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-22 16:03:12.214][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-22 16:03:12.216][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-22 16:03:12.218][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-22 16:03:12.219][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-22 16:03:12.221][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-22 16:03:12.223][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-22 16:03:12.224][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-22 16:03:12.226][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-22 16:03:12.228][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-22 16:03:12.230][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-22 16:03:12.232][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-22 16:03:12.233][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-22 16:03:12.235][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-22 16:03:12.237][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-22 16:03:12.239][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-22 16:03:12.240][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-22 16:03:12.242][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-22 16:03:12.244][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-22 16:03:12.246][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-22 16:03:12.247][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-22 16:03:12.249][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-22 16:03:12.251][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-22 16:03:12.252][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-22 16:03:12.254][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-22 16:03:12.256][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-22 16:03:12.257][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-22 16:03:12.259][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-22 16:03:12.261][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-22 16:03:12.263][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-22 16:03:12.265][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-22 16:03:12.266][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-22 16:03:12.268][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-22 16:03:12.270][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-22 16:03:12.272][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-22 16:03:12.273][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-22 16:03:12.276][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-22 16:03:12.278][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-22 16:03:12.280][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-22 16:03:12.282][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-22 16:03:12.284][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-22 16:03:12.286][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-22 16:03:12.287][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-22 16:03:12.289][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-22 16:03:12.291][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-22 16:03:12.293][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-22 16:03:12.296][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-22 16:03:12.298][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-22 16:03:12.300][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-22 16:03:12.302][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:03:12.303][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.306][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:12.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:12.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:12.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.316][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[2025-11-22 16:03:12.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:12.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:12.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:12.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:12.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:12.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:12.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:12.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:12.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.344][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[2025-11-22 16:03:12.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:12.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:12.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.353][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[2025-11-22 16:03:12.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:12.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:12.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:12.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:12.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:12.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:12.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:12.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:12.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:12.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:12.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:12.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:12.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:12.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:12.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:12.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:12.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:12.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.408][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[2025-11-22 16:03:12.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:12.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:12.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:12.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:12.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:12.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:12.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:12.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:12.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:12.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:12.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:12.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.446][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[2025-11-22 16:03:12.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:12.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:12.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:12.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:12.458][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-11-22 16:03:12.461][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-11-22 16:03:12.464][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.465][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-11-22 16:03:12.467][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.468][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:12.470][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.471][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:12.473][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.474][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:12.476][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-11-22 16:03:12.477][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:12.479][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.480][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-11-22 16:03:12.482][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:12.483][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-11-22 16:03:12.483][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-11-22 16:03:12.485][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:12.486][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:12.488][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-22 16:03:12.489][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:12.491][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:12.492][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:12.493][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:12.495][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:12.496][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:12.498][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-11-22 16:03:12.498][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-11-22 16:03:12.499][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:12.501][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:12.502][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.504][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:12.505][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-11-22 16:03:12.508][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.510][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-11-22 16:03:12.511][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.513][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:12.515][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.516][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:12.518][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.519][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:12.521][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-22 16:03:12.522][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:12.524][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.525][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-11-22 16:03:12.527][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:12.528][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-11-22 16:03:12.528][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-11-22 16:03:12.528][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-11-22 16:03:12.528][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-11-22 16:03:12.528][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-11-22 16:03:12.528][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-11-22 16:03:12.530][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:12.531][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:12.533][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-22 16:03:12.534][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:12.535][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:12.537][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:12.538][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:12.540][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:12.541][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:12.543][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:12.543][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-22 16:03:12.544][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:12.545][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:12.547][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.548][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:12.550][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-11-22 16:03:12.553][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:12.555][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-11-22 16:03:12.556][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.558][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:12.559][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.561][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:12.562][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.563][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:12.565][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-22 16:03:12.566][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:12.568][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.569][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-11-22 16:03:12.571][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:12.572][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-11-22 16:03:12.572][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:12.572][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:12.572][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:12.572][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:12.572][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:12.572][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:12.572][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:12.572][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:12.572][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:12.572][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-11-22 16:03:12.572][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:12.572][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:12.572][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-22 16:03:12.574][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:12.576][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:12.576][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:03:12.576][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:03:12.577][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-11-22 16:03:12.579][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:12.580][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:12.581][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:12.583][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:12.584][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:12.586][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:12.587][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:12.587][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-22 16:03:12.587][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-11-22 16:03:12.589][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:12.590][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:12.591][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.593][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-11-22 16:03:12.595][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-11-22 16:03:12.602][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.603][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-11-22 16:03:12.604][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.605][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:12.606][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.608][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:12.609][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.610][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:12.611][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-22 16:03:12.612][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:12.614][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.615][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-11-22 16:03:12.616][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:12.617][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-11-22 16:03:12.617][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-11-22 16:03:12.619][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:12.620][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:12.621][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-11-22 16:03:12.622][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:12.623][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:12.625][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:12.626][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:12.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:12.628][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:12.629][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:12.629][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-22 16:03:12.629][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-11-22 16:03:12.631][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:12.632][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:12.633][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:12.634][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-11-22 16:03:12.636][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-11-22 16:03:12.638][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-22 16:03:12.640][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-22 16:03:12.642][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-11-22 16:03:12.643][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-22 16:03:12.645][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-11-22 16:03:12.651][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2025-11-22 16:03:12.661][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2025-11-22 16:03:12.666][biodb::testThat]
biodb.INFO [2025-11-22 16:03:12.667][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-22 16:03:12.668][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:12.670][biodb::testThat]
biodb.TRACE[2025-11-22 16:03:12.673][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2025-11-22 16:03:12.675][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-11-22 16:03:12.678][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-11-22 16:03:12.681][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:03:12.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:12.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:12.689][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:12.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:12.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:12.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:03:12.696][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.698][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.700][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.707][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:12.709][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:12.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.711][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.713][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:12.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:12.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.718][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-22 16:03:12.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-22 16:03:12.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.723][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-22 16:03:12.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-22 16:03:12.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.732][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-22 16:03:12.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-22 16:03:12.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:03:12.767][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2025-11-22 16:03:12.770][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-22 16:03:12.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:12.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.775][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-22 16:03:12.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-22 16:03:12.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.780][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:12.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-22 16:03:12.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.785][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:03:12.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:03:12.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.790][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:03:12.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:03:12.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.795][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-22 16:03:12.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-22 16:03:12.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.800][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-22 16:03:12.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-22 16:03:12.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.816][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-22 16:03:12.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-22 16:03:12.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.859][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-22 16:03:12.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-22 16:03:12.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.864][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-22 16:03:12.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-22 16:03:12.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.869][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-22 16:03:12.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-22 16:03:12.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.898][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.900][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.902][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.919][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:12.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:12.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.925][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:12.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:12.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.930][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:12.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:12.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.936][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:12.937][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:12.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.940][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.941][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:12.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:12.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.956][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:12.958][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:12.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.960][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:12.967][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:12.968][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:03:12.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:12.971][ef$get] fields variable is a list.
biodb.INFO [2025-11-22 16:03:12.981][biodb::testThat]
biodb.INFO [2025-11-22 16:03:12.982][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-22 16:03:12.983][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:12.985][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:12.988][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-11-22 16:03:12.990][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-11-22 16:03:12.992][self$getFolder] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75".
fscache.INFO [2025-11-22 16:03:12.994][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-22 16:03:12.995][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:12.996][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:12.998][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:12.999][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-22 16:03:13.000][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-11-22 16:03:13.064][biodb::testThat]
biodb.INFO [2025-11-22 16:03:13.065][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-22 16:03:13.066][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:13.067][biodb::testThat]
biodb.INFO [2025-11-22 16:03:13.075][biodb::testThat]
biodb.INFO [2025-11-22 16:03:13.077][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-22 16:03:13.078][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:13.079][biodb::testThat]
biodb.WARN [2025-11-22 16:03:13.083][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-11-22 16:03:13.088][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-11-22 16:03:13.099][biodb::testThat]
biodb.INFO [2025-11-22 16:03:13.100][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-22 16:03:13.101][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:13.103][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:13.107][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-11-22 16:03:13.109][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-11-22 16:03:13.111][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-22 16:03:13.112][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:03:13.113][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:13.115][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:03:13.116][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-22 16:03:13.117][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-11-22 16:03:13.174][biodb::testThat]
biodb.INFO [2025-11-22 16:03:13.176][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-22 16:03:13.177][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:13.178][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-11-22 16:03:13.238][biodb::testThat]
biodb.INFO [2025-11-22 16:03:13.239][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-22 16:03:13.240][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:13.241][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-11-22 16:03:13.300][biodb::testThat]
biodb.INFO [2025-11-22 16:03:13.301][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-22 16:03:13.302][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:13.303][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-11-22 16:03:13.362][biodb::testThat]
biodb.INFO [2025-11-22 16:03:13.364][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-22 16:03:13.365][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:13.366][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-11-22 16:03:13.432][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-22 16:03:13.434][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2025-11-22 16:03:13.435][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-22 16:03:13.436][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:13.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:13.438][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:13.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:13.441][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:13.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ 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 Patched (2025-11-05 r88990)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNcbi/DESCRIPTION’ ... OK
* this is package ‘biodbNcbi’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNcbi’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    testref   7.6Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NcbiCcdsConn.Rd: BiodbFactory, BiodbConn
  NcbiCcdsEntry.Rd: BiodbHtmlEntry
  NcbiEntrezConn.Rd: BiodbConn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
  
  [ FAIL 31 | WARN 1 | SKIP 1 | PASS 247 ]
  Error:
  ! Test failures.
  Warning message:
  In fun(libname, pkgname) :
    Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
    version 3.23
  Execution halted
* DONE

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

Installation output

biodbNcbi.Rcheck/00install.out

* installing *source* package ‘biodbNcbi’ ...
** this is package ‘biodbNcbi’ version ‘1.14.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNcbi)