Back to Long Tests report for BioC 3.22

This page was generated on 2025-09-27 23:55 -0400 (Sat, 27 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4832
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4620
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 6/29HostnameOS / ArchCHECK
biodbHmdb 1.15.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-09-27 09:55 -0400 (Sat, 27 Sep 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: fa89c02
git_last_commit_date: 2025-07-24 10:45:35 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on lconway

To the developers/maintainers of the biodbHmdb 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: biodbHmdb
Version: 1.15.1
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 biodbHmdb_1.15.1.tar.gz
StartedAt: 2025-09-27 16:01:22 -0400 (Sat, 27 Sep 2025)
EndedAt: 2025-09-27 16:02:26 -0400 (Sat, 27 Sep 2025)
EllapsedTime: 63.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-09-27 16:02:22.683][biodb::testContext]
biodb.INFO [2025-09-27 16:02:22.686][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-27 16:02:22.687][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-09-27 16:02:22.688][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-27 16:02:22.689][biodb::testContext]
biodb.INFO [2025-09-27 16:02:22.694][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-09-27 16:02:22.696][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-09-27 16:02:22.702][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-27 16:02:22.702][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-27 16:02:22.703][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-27 16:02:22.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.706][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-27 16:02:22.719][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-27 16:02:22.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.723][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-27 16:02:22.724][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-27 16:02:22.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.727][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-27 16:02:22.727][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-27 16:02:22.737][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-27 16:02:22.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.739][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[2025-09-27 16:02:22.739][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-27 16:02:22.740][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-27 16:02:22.741][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-27 16:02:22.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.743][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-27 16:02:22.744][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-27 16:02:22.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.747][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-27 16:02:22.748][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-27 16:02:22.749][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-27 16:02:22.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.751][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-27 16:02:22.752][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-27 16:02:22.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.755][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-27 16:02:22.756][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-27 16:02:22.757][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-27 16:02:22.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.759][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-27 16:02:22.760][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-27 16:02:22.761][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-27 16:02:22.762][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-27 16:02:22.762][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-27 16:02:22.763][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-27 16:02:22.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.765][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[2025-09-27 16:02:22.766][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-27 16:02:22.767][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-27 16:02:22.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.770][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-27 16:02:22.770][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-27 16:02:22.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.772][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[2025-09-27 16:02:22.773][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-27 16:02:22.774][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-27 16:02:22.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.777][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-27 16:02:22.778][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-27 16:02:22.778][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-27 16:02:22.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.780][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[2025-09-27 16:02:22.781][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-27 16:02:22.782][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-27 16:02:22.799][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-27 16:02:22.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.802][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-27 16:02:22.803][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-27 16:02:22.804][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-27 16:02:22.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.808][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-27 16:02:22.834][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:22.847][self$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[2025-09-27 16:02:22.848][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.849][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:02:22.850][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.851][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:02:22.852][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:22.852][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:02:22.853][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-27 16:02:22.854][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:02:22.855][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.856][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-27 16:02:22.857][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:02:22.858][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:22.858][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.859][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-27 16:02:22.859][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-27 16:02:22.859][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-27 16:02:22.859][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-27 16:02:22.859][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-27 16:02:22.860][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:02:22.861][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:22.862][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:22.862][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:02:22.863][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:22.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:22.865][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:02:22.866][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:22.867][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:02:22.867][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:02:22.868][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:22.869][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:22.870][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-27 16:02:22.872][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:22.872][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-27 16:02:22.873][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.874][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:02:22.875][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.876][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:02:22.877][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:22.877][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:02:22.878][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-27 16:02:22.879][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:02:22.884][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.885][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-27 16:02:22.886][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:02:22.887][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:22.888][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.889][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-27 16:02:22.889][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-27 16:02:22.889][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-27 16:02:22.889][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-27 16:02:22.889][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-27 16:02:22.890][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:02:22.890][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:22.891][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:22.892][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:02:22.893][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:22.893][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:22.894][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:02:22.895][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:22.896][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:02:22.897][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:02:22.897][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:22.898][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:22.899][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-27 16:02:22.901][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.901][self$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[2025-09-27 16:02:22.902][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.903][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:02:22.904][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.905][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:02:22.906][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:22.906][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:02:22.907][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-27 16:02:22.908][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:02:22.909][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:22.910][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-27 16:02:22.910][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:02:22.911][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:22.912][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.913][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:22.914][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:02:22.915][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:22.915][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:22.916][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:02:22.917][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:22.918][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:22.918][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:02:22.919][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:22.920][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:02:22.921][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:02:22.922][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:22.922][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:22.923][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-27 16:02:22.925][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.926][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-27 16:02:22.927][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.927][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:02:22.928][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.929][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:02:22.930][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:22.931][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:02:22.931][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-27 16:02:22.932][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:02:22.933][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:22.934][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-27 16:02:22.935][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:02:22.936][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:22.936][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.937][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:22.938][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:02:22.939][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:22.939][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:22.940][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:02:22.941][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:22.942][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:22.942][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:02:22.943][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:22.944][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:02:22.945][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:02:22.945][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:22.946][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:22.949][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-27 16:02:22.949][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.950][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[2025-09-27 16:02:22.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.978][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[2025-09-27 16:02:22.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.984][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[2025-09-27 16:02:22.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.995][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[2025-09-27 16:02:22.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:23.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:23.006][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-27 16:02:23.009][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-27 16:02:23.010][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-27 16:02:23.011][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-27 16:02:23.012][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-27 16:02:23.013][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-27 16:02:23.018][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-27 16:02:23.019][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-27 16:02:23.020][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-27 16:02:23.021][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-27 16:02:23.022][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-27 16:02:23.023][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-27 16:02:23.024][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-27 16:02:23.025][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-27 16:02:23.026][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-27 16:02:23.027][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-27 16:02:23.028][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-27 16:02:23.029][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-27 16:02:23.030][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-27 16:02:23.031][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-27 16:02:23.033][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-27 16:02:23.034][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-27 16:02:23.035][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-27 16:02:23.036][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-27 16:02:23.037][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-27 16:02:23.038][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-27 16:02:23.039][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-27 16:02:23.040][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-27 16:02:23.041][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-27 16:02:23.042][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-27 16:02:23.043][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-27 16:02:23.044][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-27 16:02:23.045][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-27 16:02:23.046][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-27 16:02:23.047][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-27 16:02:23.048][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-27 16:02:23.049][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-27 16:02:23.051][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-27 16:02:23.052][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-27 16:02:23.053][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-27 16:02:23.054][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-27 16:02:23.055][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-27 16:02:23.056][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-27 16:02:23.057][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-27 16:02:23.058][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-27 16:02:23.059][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-27 16:02:23.060][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-27 16:02:23.061][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-27 16:02:23.063][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-27 16:02:23.064][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-27 16:02:23.065][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-27 16:02:23.066][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-27 16:02:23.067][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-27 16:02:23.068][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-27 16:02:23.069][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-27 16:02:23.070][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-27 16:02:23.071][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-27 16:02:23.072][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-27 16:02:23.074][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-27 16:02:23.075][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-27 16:02:23.076][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-27 16:02:23.077][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-27 16:02:23.078][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-27 16:02:23.079][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-27 16:02:23.080][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-27 16:02:23.081][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-27 16:02:23.082][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-27 16:02:23.083][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-27 16:02:23.084][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-27 16:02:23.086][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-27 16:02:23.087][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-27 16:02:23.088][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-27 16:02:23.089][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-27 16:02:23.090][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-27 16:02:23.092][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-27 16:02:23.093][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-27 16:02:23.094][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-27 16:02:23.095][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-27 16:02:23.096][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-27 16:02:23.097][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-27 16:02:23.098][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-27 16:02:23.099][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-27 16:02:23.100][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-27 16:02:23.104][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-27 16:02:23.106][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-09-27 16:02:23.108][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-27 16:02:23.109][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.110][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:23.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:23.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:23.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:23.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:23.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:23.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:23.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:23.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:23.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:23.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:23.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:23.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.135][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[2025-09-27 16:02:23.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:23.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:23.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.140][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[2025-09-27 16:02:23.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:23.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:23.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:23.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:23.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:23.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.154][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[2025-09-27 16:02:23.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:23.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:23.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:23.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:23.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:23.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:23.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:23.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:23.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:23.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:23.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:23.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:23.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:23.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:23.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:23.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:23.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:23.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:23.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:23.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:23.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:23.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:23.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:23.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.194][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[2025-09-27 16:02:23.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:23.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:23.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2025-09-27 16:02:23.200][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-09-27 16:02:23.207][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-09-27 16:02:23.219][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-09-27 16:02:23.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:23.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:23.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:23.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:23.227][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-09-27 16:02:23.236][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-09-27 16:02:23.238][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:23.239][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-09-27 16:02:23.239][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:23.241][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:02:23.242][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:23.242][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-09-27 16:02:23.243][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:23.244][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:02:23.245][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-27 16:02:23.246][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:02:23.247][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:23.248][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-09-27 16:02:23.249][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:02:23.250][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-09-27 16:02:23.250][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-09-27 16:02:23.250][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-09-27 16:02:23.250][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-09-27 16:02:23.250][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-09-27 16:02:23.250][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-09-27 16:02:23.250][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-09-27 16:02:23.250][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-09-27 16:02:23.250][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-09-27 16:02:23.250][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-09-27 16:02:23.250][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-09-27 16:02:23.250][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-09-27 16:02:23.250][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-09-27 16:02:23.250][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-09-27 16:02:23.250][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-09-27 16:02:23.250][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-09-27 16:02:23.250][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-09-27 16:02:23.250][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-09-27 16:02:23.251][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:23.252][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-27 16:02:23.252][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-09-27 16:02:23.252][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-09-27 16:02:23.253][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-27 16:02:23.254][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:23.255][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:23.255][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:02:23.256][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:23.257][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:23.258][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:02:23.259][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-09-27 16:02:23.259][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-09-27 16:02:23.260][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:02:23.260][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:02:23.261][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:23.262][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:23.267][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-09-27 16:02:23.268][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-27 16:02:23.270][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-27 16:02:23.271][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-27 16:02:23.272][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-27 16:02:23.295][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-09-27 16:02:23.307][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-09-27 16:02:23.313][biodb::testThat]
biodb.INFO [2025-09-27 16:02:23.314][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-09-27 16:02:23.315][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:02:23.316][biodb::testThat]
biodb.TRACE[2025-09-27 16:02:23.319][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-09-27 16:02:23.320][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-09-27 16:02:23.323][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-09-27 16:02:23.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-27 16:02:23.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:23.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:23.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:23.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:23.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:23.344][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.TRACE[2025-09-27 16:02:23.352][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.353][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.355][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.368][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.369][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.371][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.392][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.397][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-27 16:02:23.398][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-27 16:02:23.399][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.400][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.401][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-27 16:02:23.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-27 16:02:23.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.404][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:23.405][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:23.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.407][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.408][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:23.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:23.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.411][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-27 16:02:23.412][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-27 16:02:23.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.414][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-27 16:02:23.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-27 16:02:23.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.418][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.418][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.420][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.433][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:23.434][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:23.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.435][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.436][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:23.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:23.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.439][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.440][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.442][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.443][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.446][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:23.447][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:23.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.448][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.449][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:23.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:23.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.452][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:23.453][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:23.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.455][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.456][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:23.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:23.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.459][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:23.460][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:23.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.461][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.462][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:23.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:23.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.465][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:23.466][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:23.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.467][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.468][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:23.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:23.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.471][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:23.472][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:23.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.473][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.474][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:23.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:23.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.477][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:23.478][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:23.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.479][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:23.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:23.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.483][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:23.484][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:23.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.485][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.486][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:23.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:23.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.489][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-27 16:02:23.490][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-27 16:02:23.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.492][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.493][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-27 16:02:23.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-27 16:02:23.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.496][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-27 16:02:23.496][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-27 16:02:23.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.498][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.499][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-27 16:02:23.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-27 16:02:23.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.502][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-09-27 16:02:23.503][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:23.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.504][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.505][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-09-27 16:02:23.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:23.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.577][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-27 16:02:23.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-27 16:02:23.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.581][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-27 16:02:23.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-27 16:02:23.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.584][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-27 16:02:23.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-27 16:02:23.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.587][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:23.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:23.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.590][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:23.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:23.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.593][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:23.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:23.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-27 16:02:23.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-27 16:02:23.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-27 16:02:23.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-27 16:02:23.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-27 16:02:23.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-27 16:02:23.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.614][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:23.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:23.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.616][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:23.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:23.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.619][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:23.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:23.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.622][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:23.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:23.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.625][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:23.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:23.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.628][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:23.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:23.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.631][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:23.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:23.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.634][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:23.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:23.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.636][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:23.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:23.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.639][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-27 16:02:23.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-27 16:02:23.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.642][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-27 16:02:23.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-27 16:02:23.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.645][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-27 16:02:23.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-27 16:02:23.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.652][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:23.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:23.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.655][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:23.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:23.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.658][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:23.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:23.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.661][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:23.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:23.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:23.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:23.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.666][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:23.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:23.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.669][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:23.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:23.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.672][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:23.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:23.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.675][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:23.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:23.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.678][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:23.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:23.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.681][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:23.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:23.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.684][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:23.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:23.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:23.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:23.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:23.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:23.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:23.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:23.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.695][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:23.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:23.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:23.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:23.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:23.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:23.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.704][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.707][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.710][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.713][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.716][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.719][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.722][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-27 16:02:23.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-27 16:02:23.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.725][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-27 16:02:23.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-27 16:02:23.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.728][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-27 16:02:23.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-27 16:02:23.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.731][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-09-27 16:02:23.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:23.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.734][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:23.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:23.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.737][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:23.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:23.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.739][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:23.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:23.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.743][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-09-27 16:02:23.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:23.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:23.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:23.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.765][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:23.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:23.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.768][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:23.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:23.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:23.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:23.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.775][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:23.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:23.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.778][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-27 16:02:23.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-27 16:02:23.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.782][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-27 16:02:23.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-27 16:02:23.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.789][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-27 16:02:23.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-27 16:02:23.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-27 16:02:23.813][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-09-27 16:02:23.815][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-27 16:02:23.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-27 16:02:23.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.819][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-27 16:02:23.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-27 16:02:23.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.822][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-27 16:02:23.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-27 16:02:23.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.825][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-27 16:02:23.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-27 16:02:23.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.838][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-27 16:02:23.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-27 16:02:23.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.873][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-27 16:02:23.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-27 16:02:23.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.877][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-27 16:02:23.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-27 16:02:23.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.880][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-27 16:02:23.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-27 16:02:23.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.901][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.902][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.903][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:23.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:23.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.915][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.919][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.922][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.925][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.926][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.928][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.929][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:23.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.943][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.949][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.950][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.951][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:23.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.962][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.965][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.973][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.976][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.977][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.979][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.979][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:23.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-27 16:02:23.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-27 16:02:23.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-27 16:02:23.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-27 16:02:23.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:23.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-27 16:02:23.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-27 16:02:23.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:23.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.000][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-27 16:02:24.001][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-27 16:02:24.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.002][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-27 16:02:24.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-27 16:02:24.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.013][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:24.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:24.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.016][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:24.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:24.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.020][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:24.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:24.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.023][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:24.024][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:24.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.025][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.026][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:24.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:24.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.036][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:24.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:24.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.039][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:24.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:24.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:24.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:24.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.045][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:24.046][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:24.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.048][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.048][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:24.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:24.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.058][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-27 16:02:24.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-27 16:02:24.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.061][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-27 16:02:24.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-27 16:02:24.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.065][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-27 16:02:24.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-27 16:02:24.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.068][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-27 16:02:24.069][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-27 16:02:24.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.071][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.071][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-27 16:02:24.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-27 16:02:24.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.086][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:24.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:24.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.090][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:24.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:24.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.093][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:24.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:24.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.097][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:24.098][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:24.099][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.100][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.101][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:24.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:24.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.112][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-27 16:02:24.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-27 16:02:24.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.116][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-27 16:02:24.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-27 16:02:24.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.120][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-27 16:02:24.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-27 16:02:24.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.123][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-27 16:02:24.124][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-27 16:02:24.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.126][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.127][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-27 16:02:24.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-27 16:02:24.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:24.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:24.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:24.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:24.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.145][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:24.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:24.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.148][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:24.149][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:24.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.151][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:24.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:24.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.162][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:24.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:24.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.165][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:24.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:24.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.168][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:24.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:24.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.172][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:24.173][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:24.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.174][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.175][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:24.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:24.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.186][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:24.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:24.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.189][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:24.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:24.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.192][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:24.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:24.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.199][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:24.200][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:24.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.201][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.202][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:24.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:24.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.212][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:24.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:24.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.215][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:24.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:24.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.217][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:24.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:24.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.220][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:24.221][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:24.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.222][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.223][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:24.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:24.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.233][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-27 16:02:24.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-27 16:02:24.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.236][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-27 16:02:24.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-27 16:02:24.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.239][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-27 16:02:24.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-27 16:02:24.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.242][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-27 16:02:24.243][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-27 16:02:24.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.244][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.245][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-27 16:02:24.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-27 16:02:24.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.255][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:24.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:24.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.258][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:24.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:24.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:24.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:24.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.263][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:24.264][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:24.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.266][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.266][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:24.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:24.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.276][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:24.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:24.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.279][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:24.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:24.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.283][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:24.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:24.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.286][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:24.286][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:24.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.288][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.288][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:24.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:24.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.302][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:24.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:24.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.305][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:24.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:24.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.308][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:24.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:24.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.311][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:24.312][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:24.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.313][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.314][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:24.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:24.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.324][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:24.325][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:24.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.326][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.331][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-27 16:02:24.331][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-27 16:02:24.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.333][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.337][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:24.338][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:24.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.340][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.344][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-27 16:02:24.344][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-27 16:02:24.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.346][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.350][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:24.351][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-27 16:02:24.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.352][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.356][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:24.357][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-27 16:02:24.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.358][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.362][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:24.363][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-27 16:02:24.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.365][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.369][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:24.370][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-27 16:02:24.371][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.372][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.376][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-27 16:02:24.377][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-27 16:02:24.377][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.378][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.382][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:24.383][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:24.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.384][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.388][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:24.389][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:24.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.390][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.394][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:24.395][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:24.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.397][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.401][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:24.401][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-27 16:02:24.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.403][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.407][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:24.407][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-27 16:02:24.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.413][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.417][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:24.418][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:24.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.419][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.424][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:24.425][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-27 16:02:24.425][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.426][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.430][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:24.431][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:24.431][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.432][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.436][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-27 16:02:24.437][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-27 16:02:24.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.438][ef$get] fields variable is a list.
biodb.INFO [2025-09-27 16:02:24.445][biodb::testThat]
biodb.INFO [2025-09-27 16:02:24.446][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-09-27 16:02:24.447][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:02:24.447][biodb::testThat]
biodb.DEBUG[2025-09-27 16:02:24.457][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-09-27 16:02:24.459][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-27 16:02:24.461][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-27 16:02:24.482][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-09-27 16:02:24.483][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-09-27 16:02:24.484][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-09-27 16:02:24.517][biodb::testThat]
biodb.INFO [2025-09-27 16:02:24.518][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-09-27 16:02:24.519][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:02:24.520][biodb::testThat]
biodb.TRACE[2025-09-27 16:02:24.522][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:24.523][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:24.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.525][ef$get] fields variable is a list.
biodb.DEBUG[2025-09-27 16:02:24.526][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-09-27 16:02:24.544][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-09-27 16:02:24.576][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-27 16:02:24.578][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-27 16:02:24.579][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-09-27 16:02:24.580][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-09-27 16:02:24.593][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-09-27 16:02:24.611][biodb::testThat]
biodb.INFO [2025-09-27 16:02:24.612][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-09-27 16:02:24.613][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:02:24.613][biodb::testThat]
biodb.DEBUG[2025-09-27 16:02:24.620][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-09-27 16:02:24.621][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-27 16:02:24.623][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-27 16:02:24.624][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-09-27 16:02:24.625][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-09-27 16:02:24.626][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-09-27 16:02:24.637][biodb::testThat]
biodb.INFO [2025-09-27 16:02:24.638][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-09-27 16:02:24.639][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:02:24.640][biodb::testThat]
biodb.DEBUG[2025-09-27 16:02:24.643][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-09-27 16:02:24.643][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-27 16:02:24.645][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-27 16:02:24.646][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-09-27 16:02:24.647][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-09-27 16:02:24.648][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-09-27 16:02:24.659][biodb::testThat]
biodb.INFO [2025-09-27 16:02:24.660][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-09-27 16:02:24.661][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:02:24.662][biodb::testThat]
biodb.INFO [2025-09-27 16:02:24.673][biodb::testThat]
biodb.INFO [2025-09-27 16:02:24.674][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-09-27 16:02:24.675][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:02:24.676][biodb::testThat]
biodb.INFO [2025-09-27 16:02:24.692][biodb::testThat]
biodb.INFO [2025-09-27 16:02:24.692][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-09-27 16:02:24.693][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:02:24.694][biodb::testThat]
biodb.INFO [2025-09-27 16:02:24.706][biodb::testThat]
biodb.INFO [2025-09-27 16:02:24.707][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-09-27 16:02:24.707][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:02:24.708][biodb::testThat]
biodb.TRACE[2025-09-27 16:02:24.729][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:24.730][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:24.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.731][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.732][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-27 16:02:24.733][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-27 16:02:24.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.734][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.735][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:24.736][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:24.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.737][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.738][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:24.739][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:24.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.740][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.741][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-27 16:02:24.742][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-27 16:02:24.743][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.744][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:24.744][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:24.745][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-27 16:02:24.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:24.747][ef$get] fields variable is a list.
biodb.INFO [2025-09-27 16:02:24.748][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-09-27 16:02:24.748][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-09-27 16:02:24.749][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-27 16:02:24.750][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:24.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:24.751][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:24.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:24.753][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:24.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:42:1'): RT unit is defined when there is an RT value. ──
Error in `private$doExtractDownload()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getBiodb()$getFactory()$getEntry(...)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doExtractDownload()
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by searchable field ──
Error in `cch$getTmpFolderPath()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, 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$download()
 8.             └─private$doExtractDownload()
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by name. ──
Error in `cch$getTmpFolderPath()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$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$getEntryContent(ids)
 7.           └─self$download()
 8.             └─private$doExtractDownload()
── Error ('test_long_100_generic.R:42:1'): We can load an entry from the database. ──
Error in `cch$getTmpFolderPath()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, 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$getEntryContent(ids)
 8.             └─self$download()
 9.               └─private$doExtractDownload()
── Error ('test_long_100_generic.R:42:1'): We can get a URL pointing to the entry page. ──
Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbHmdb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:42:1'): We can get a URL pointing to the entry image. ──
Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbHmdb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:42:1'): The entry page URL can be downloaded. ──
Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbHmdb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbHmdb (local) FUN(X[[i]], ...)

[ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]
Error: Test failures
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 biodbHmdb_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.15.1’
* 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 ‘biodbHmdb’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... 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:
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
   5.       └─base::vapply(id, fct, FUN.VALUE = "")
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  
  [ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.15.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c EntryMaker.cpp -o EntryMaker.o
EntryMaker.cpp:6:5: warning: field 'accession_tag' will be initialized after field 'closed' [-Wreorder-ctor]
    accession_tag("<accession>", "</accession>"),
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    closed(true)
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FileEntryMaker.cpp -o FileEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c TagDetector.cpp -o TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c XmlSplitter.cpp -o XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractXmlEntries.cpp -o extractXmlEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-TagDetector.cpp -o test-100-TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)