Back to Long Tests report for BioC 3.22

This page was generated on 2026-03-07 23:55 -0500 (Sat, 07 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4892
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4684
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 6/31HostnameOS / ArchCHECK
biodbHmdb 1.16.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-03-07 09:55 -0500 (Sat, 07 Mar 2026)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_22
git_last_commit: 4102973
git_last_commit_date: 2025-10-29 11:13:48 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on nebbiolo2

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: 1.16.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
StartedAt: 2026-03-07 16:01:09 -0500 (Sat, 07 Mar 2026)
EndedAt: 2026-03-07 16:02:17 -0500 (Sat, 07 Mar 2026)
EllapsedTime: 68.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


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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 [2026-03-07 16:02:13.802][biodb::testContext]
biodb.INFO [2026-03-07 16:02:13.804][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-07 16:02:13.805][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-03-07 16:02:13.806][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-07 16:02:13.807][biodb::testContext]
biodb.INFO [2026-03-07 16:02:13.812][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-07 16:02:13.814][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2026-03-07 16:02:13.820][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:02:13.821][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-07 16:02:13.822][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-07 16:02:13.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:13.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:13.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:13.825][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-07 16:02:13.841][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-07 16:02:13.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:13.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:13.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:13.844][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-07 16:02:13.845][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-07 16:02:13.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:13.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:13.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:13.849][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-07 16:02:13.850][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-07 16:02:13.850][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-07 16:02:13.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:13.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:13.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:13.854][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-07 16:02:13.855][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-07 16:02:13.856][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-07 16:02:13.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:13.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:13.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:13.859][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-07 16:02:13.860][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-07 16:02:13.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:13.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:13.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:13.863][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-07 16:02:13.864][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-07 16:02:13.865][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-07 16:02:13.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:13.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:13.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:13.868][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-07 16:02:13.869][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-07 16:02:13.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:13.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:13.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:13.873][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-07 16:02:13.874][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-07 16:02:13.875][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-07 16:02:13.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:13.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:13.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:13.878][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-07 16:02:13.879][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-07 16:02:13.880][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-07 16:02:13.881][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-07 16:02:13.882][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-07 16:02:13.883][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-07 16:02:13.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:13.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:13.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:13.886][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-07 16:02:13.887][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-07 16:02:13.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:13.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:13.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:13.890][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-07 16:02:13.891][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-07 16:02:13.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:13.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:13.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:13.894][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-07 16:02:13.895][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-07 16:02:13.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:13.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:13.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:13.899][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-07 16:02:13.900][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-07 16:02:13.901][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-07 16:02:13.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:13.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:13.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:13.904][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-07 16:02:13.905][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-07 16:02:13.910][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-07 16:02:13.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:13.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:13.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:13.913][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-07 16:02:13.914][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-07 16:02:13.915][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-07 16:02:13.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:13.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:13.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:13.921][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-07 16:02:13.950][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:13.970][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-03-07 16:02:13.971][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:13.972][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:13.973][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:13.973][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:13.974][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:13.975][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:13.976][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-07 16:02:13.977][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:13.978][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:13.979][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-07 16:02:13.980][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:13.981][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:13.982][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:13.983][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:13.983][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:02:13.983][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:02:13.983][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-07 16:02:13.983][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-07 16:02:13.983][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:13.984][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:13.985][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:13.986][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:13.987][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:13.988][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:13.989][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:13.990][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:13.990][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:13.991][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:13.992][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:13.993][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:13.994][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-07 16:02:13.996][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:13.997][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-07 16:02:13.998][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:13.999][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:13.999][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:14.000][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:14.001][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:14.002][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:14.003][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-07 16:02:14.004][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:14.005][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:14.006][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-07 16:02:14.007][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:14.008][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:14.009][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:14.009][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:14.009][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:02:14.009][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:02:14.009][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-07 16:02:14.009][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-07 16:02:14.010][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:14.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:14.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:14.013][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:14.014][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:14.015][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:14.016][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:14.017][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:14.017][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:14.018][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:14.019][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:14.020][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:14.021][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-07 16:02:14.023][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:14.024][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-03-07 16:02:14.025][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:14.025][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:14.026][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:14.027][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:14.028][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:14.029][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:14.030][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-07 16:02:14.031][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:14.032][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:14.033][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-07 16:02:14.034][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:14.035][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:14.035][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:14.036][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:14.037][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:14.038][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:14.039][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:14.040][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:14.041][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:14.042][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:14.042][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:14.043][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:14.044][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:14.045][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:14.046][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:14.047][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:14.048][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-07 16:02:14.049][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:14.050][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-07 16:02:14.051][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:14.052][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:14.053][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:14.054][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:02:14.055][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:14.056][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:14.057][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-07 16:02:14.058][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:14.059][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:14.060][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-07 16:02:14.060][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:14.061][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:14.062][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:14.063][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:14.064][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:02:14.065][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:14.066][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:14.067][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:14.068][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:14.068][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:14.069][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:14.070][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:14.071][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:14.072][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:14.073][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:14.074][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:14.077][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:02:14.078][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.120][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[2026-03-07 16:02:14.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.146][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-07 16:02:14.150][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-07 16:02:14.151][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-07 16:02:14.152][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-07 16:02:14.154][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-07 16:02:14.155][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-07 16:02:14.156][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-07 16:02:14.157][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-07 16:02:14.159][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-07 16:02:14.160][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-07 16:02:14.165][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-07 16:02:14.166][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-07 16:02:14.168][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-07 16:02:14.169][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-07 16:02:14.170][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-07 16:02:14.171][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-07 16:02:14.173][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-07 16:02:14.174][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-07 16:02:14.175][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-07 16:02:14.176][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-07 16:02:14.178][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-07 16:02:14.179][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-07 16:02:14.180][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-07 16:02:14.181][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-07 16:02:14.183][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-07 16:02:14.184][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-07 16:02:14.185][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-07 16:02:14.187][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-07 16:02:14.188][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-07 16:02:14.189][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-07 16:02:14.190][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-07 16:02:14.192][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-07 16:02:14.193][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-07 16:02:14.194][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-07 16:02:14.195][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-07 16:02:14.197][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-07 16:02:14.198][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-07 16:02:14.199][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-07 16:02:14.201][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-07 16:02:14.202][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-07 16:02:14.203][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-07 16:02:14.204][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-07 16:02:14.206][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-07 16:02:14.207][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-07 16:02:14.208][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-07 16:02:14.210][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-07 16:02:14.211][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-07 16:02:14.212][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-07 16:02:14.213][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-07 16:02:14.215][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-07 16:02:14.216][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-07 16:02:14.224][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-07 16:02:14.226][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-07 16:02:14.228][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-07 16:02:14.229][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-07 16:02:14.231][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-07 16:02:14.232][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-07 16:02:14.234][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-07 16:02:14.235][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-07 16:02:14.236][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-07 16:02:14.238][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-07 16:02:14.239][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-07 16:02:14.241][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-07 16:02:14.242][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-07 16:02:14.244][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-07 16:02:14.245][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-07 16:02:14.246][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-07 16:02:14.248][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-07 16:02:14.249][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-07 16:02:14.251][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-07 16:02:14.252][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-07 16:02:14.254][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-07 16:02:14.255][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-07 16:02:14.256][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-07 16:02:14.258][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-07 16:02:14.259][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-07 16:02:14.261][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-07 16:02:14.262][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-07 16:02:14.263][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-07 16:02:14.265][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-07 16:02:14.266][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-07 16:02:14.268][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-07 16:02:14.269][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-07 16:02:14.276][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-07 16:02:14.278][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-07 16:02:14.282][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:02:14.282][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.284][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:14.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:14.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:14.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:14.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:14.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:14.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:14.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:14.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:14.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:14.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:14.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:14.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:14.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:14.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:14.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:14.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:14.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:14.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:14.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:14.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:14.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:14.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:14.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:14.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:14.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:14.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:14.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:14.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:14.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:14.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:14.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:14.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2026-03-07 16:02:14.405][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2026-03-07 16:02:14.413][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2026-03-07 16:02:14.427][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2026-03-07 16:02:14.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:02:14.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:14.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:14.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:02:14.435][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2026-03-07 16:02:14.444][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2026-03-07 16:02:14.446][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:14.447][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2026-03-07 16:02:14.448][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:14.449][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:02:14.450][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:14.451][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2026-03-07 16:02:14.452][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:14.452][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:02:14.453][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-07 16:02:14.454][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:02:14.455][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:14.456][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2026-03-07 16:02:14.457][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:02:14.458][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2026-03-07 16:02:14.458][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2026-03-07 16:02:14.458][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2026-03-07 16:02:14.458][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2026-03-07 16:02:14.458][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2026-03-07 16:02:14.458][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2026-03-07 16:02:14.458][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2026-03-07 16:02:14.458][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2026-03-07 16:02:14.458][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2026-03-07 16:02:14.458][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2026-03-07 16:02:14.458][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2026-03-07 16:02:14.458][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2026-03-07 16:02:14.458][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2026-03-07 16:02:14.458][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2026-03-07 16:02:14.458][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2026-03-07 16:02:14.458][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2026-03-07 16:02:14.458][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2026-03-07 16:02:14.458][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2026-03-07 16:02:14.459][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:02:14.460][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:02:14.460][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2026-03-07 16:02:14.460][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2026-03-07 16:02:14.461][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-07 16:02:14.462][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:14.463][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:14.464][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:02:14.464][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:02:14.465][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:02:14.466][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:02:14.467][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2026-03-07 16:02:14.467][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2026-03-07 16:02:14.468][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:02:14.469][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:02:14.470][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:02:14.471][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:02:14.476][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2026-03-07 16:02:14.477][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-07 16:02:14.479][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-07 16:02:14.480][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-07 16:02:14.482][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-07 16:02:14.502][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2026-03-07 16:02:14.516][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2026-03-07 16:02:14.524][biodb::testThat]
biodb.INFO [2026-03-07 16:02:14.525][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-03-07 16:02:14.526][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:14.527][biodb::testThat]
biodb.TRACE[2026-03-07 16:02:14.530][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2026-03-07 16:02:14.532][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2026-03-07 16:02:14.535][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2026-03-07 16:02:14.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-07 16:02:14.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:14.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:14.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:14.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:14.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:14.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-07 16:02:14.569][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:14.570][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:14.571][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.572][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:14.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:14.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.588][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:14.589][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:14.590][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.591][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.624][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:14.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:14.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.628][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:02:14.629][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:02:14.629][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.630][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.632][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:02:14.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:02:14.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.635][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:02:14.636][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:02:14.637][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.638][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.639][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:02:14.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:02:14.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.643][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:02:14.644][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:02:14.645][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.646][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:02:14.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:02:14.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.651][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:14.652][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:14.653][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.653][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:14.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:14.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.658][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:14.659][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:14.660][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.661][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.662][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:14.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:14.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.666][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:14.667][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:14.668][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.669][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.670][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:14.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:14.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.674][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:14.675][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:14.675][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.676][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.678][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:14.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:14.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.681][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:14.682][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:14.683][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.684][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.685][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:14.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:14.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.689][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:14.690][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:14.691][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.692][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.693][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:14.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:14.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.696][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:14.697][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:14.698][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.699][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.700][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:14.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:14.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.704][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:14.705][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:14.706][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.707][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.708][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:14.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:14.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.712][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:14.713][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:14.714][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.715][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:14.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:14.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.720][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:14.721][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:14.722][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.722][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.723][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:14.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:14.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.727][ef$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:02:14.728][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:02:14.729][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.730][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.731][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:02:14.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:02:14.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.735][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:02:14.736][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:02:14.737][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.738][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.739][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:02:14.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:02:14.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.743][ef$get] Asked field names are: super.class.
biodb.TRACE[2026-03-07 16:02:14.744][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:14.744][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.745][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.746][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2026-03-07 16:02:14.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:14.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:14.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:14.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:14.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:14.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:14.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:14.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.795][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:02:14.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:02:14.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.799][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:02:14.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:02:14.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.802][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:02:14.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:02:14.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.806][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:02:14.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:02:14.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.810][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:02:14.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:02:14.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.813][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:02:14.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:02:14.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:02:14.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:02:14.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:02:14.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:02:14.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:02:14.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:02:14.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.828][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:14.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:14.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:14.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:14.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.835][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:14.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:14.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.839][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:14.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:14.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.842][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:14.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:14.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.846][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:14.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:14.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.850][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:14.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:14.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.853][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:14.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:14.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.857][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:14.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:14.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.861][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:14.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:14.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.864][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:14.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:14.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.868][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:14.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:14.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.872][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:02:14.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:02:14.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.876][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:02:14.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:02:14.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.879][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:02:14.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:02:14.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.883][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:14.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:14.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.887][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:14.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:14.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.890][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:14.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:14.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.894][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:14.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:14.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:14.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:14.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.901][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:14.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:14.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:14.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:14.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.908][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:14.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:14.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.912][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:14.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:14.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.916][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:14.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:14.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.923][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:14.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:14.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.926][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:14.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:14.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:14.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:14.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:14.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:14.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:14.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:14.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.941][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:14.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:14.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.944][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:14.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:14.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.948][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:14.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:14.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.952][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:14.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:14.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.955][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:14.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:14.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.959][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:14.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:14.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.963][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:14.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:14.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.966][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:14.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:14.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.970][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:14.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:14.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.974][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:02:14.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:02:14.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.977][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:02:14.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:02:14.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.981][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:02:14.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:02:14.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.985][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-03-07 16:02:14.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:14.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.988][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:14.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:14.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.992][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:14.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:14.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.996][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:14.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:14.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:14.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:14.999][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-03-07 16:02:15.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:15.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.019][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:15.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:15.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.023][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:15.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:15.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:15.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:15.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.030][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:15.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:15.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.034][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:15.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:15.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.038][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:02:15.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:02:15.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.041][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:02:15.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:02:15.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.049][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:02:15.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:02:15.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-07 16:02:15.074][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2026-03-07 16:02:15.116][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-07 16:02:15.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-07 16:02:15.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.120][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-07 16:02:15.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-07 16:02:15.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.123][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-07 16:02:15.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-07 16:02:15.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.127][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-07 16:02:15.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-07 16:02:15.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.139][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:02:15.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:02:15.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.169][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:02:15.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:02:15.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.173][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:02:15.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:02:15.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.177][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:02:15.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:02:15.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.197][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.198][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.199][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.200][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.211][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:15.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:15.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.215][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:15.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:15.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.219][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:15.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:15.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.222][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:15.223][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:15.224][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.225][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.226][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:15.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:15.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:15.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:15.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:15.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:15.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:15.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:15.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.247][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:15.248][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:15.249][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.250][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.251][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:15.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:15.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.261][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:15.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:15.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.265][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:15.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:15.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.268][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:15.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:15.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.272][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:15.273][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:15.278][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.278][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.279][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:15.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:15.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:02:15.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:02:15.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:02:15.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:02:15.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:02:15.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:02:15.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.300][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:02:15.301][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:02:15.302][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.303][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:02:15.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:02:15.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.314][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:15.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:15.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.318][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:15.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:15.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.322][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:15.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:15.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.325][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:15.326][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:15.327][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.328][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.329][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:15.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:15.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.339][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:15.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:15.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:15.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:15.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.346][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:15.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:15.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.350][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:15.351][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:15.352][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.353][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.354][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:15.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:15.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.364][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:02:15.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:02:15.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.367][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:02:15.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:02:15.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.371][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:02:15.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:02:15.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.375][ef$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:02:15.376][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:02:15.377][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.378][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.379][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:02:15.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:02:15.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.389][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:15.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:15.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.392][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:15.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:15.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.396][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:15.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:15.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.400][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:15.401][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:15.402][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.402][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.403][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:15.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:15.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.413][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:02:15.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:02:15.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.417][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:02:15.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:02:15.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.421][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:02:15.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:02:15.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.424][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:02:15.425][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:02:15.426][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.427][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.428][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:02:15.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:02:15.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:15.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:15.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:15.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:15.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:15.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:15.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.453][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:15.454][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:15.454][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.455][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:15.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:15.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.467][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:15.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:15.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.470][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:15.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:15.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.474][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:15.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:15.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.478][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:15.479][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:15.480][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.481][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.481][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:15.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:15.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.492][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:15.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:15.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.495][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:15.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:15.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.499][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:15.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:15.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.503][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:15.503][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:15.504][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.505][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.506][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:15.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:15.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.516][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:15.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:15.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.520][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:15.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:15.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.524][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:15.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:15.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.527][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:15.528][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:15.529][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.530][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.531][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:15.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:15.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.541][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:02:15.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:02:15.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.545][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:02:15.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:02:15.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.548][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:02:15.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:02:15.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.552][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:02:15.553][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:02:15.554][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.555][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.556][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:02:15.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:02:15.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.566][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:15.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:15.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:15.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:15.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:15.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:15.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.577][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:15.578][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:15.579][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.580][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:15.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:15.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.594][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:15.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:15.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:15.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:15.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.601][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:15.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:15.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.605][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:15.606][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:15.607][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.608][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:15.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:15.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.619][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:02:15.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:02:15.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.622][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:02:15.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:02:15.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.626][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:02:15.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:02:15.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.630][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:02:15.631][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:02:15.632][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.632][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.633][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:02:15.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:02:15.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.644][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:02:15.645][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:02:15.645][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.646][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.650][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:02:15.651][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:02:15.652][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.653][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.657][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:02:15.657][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:02:15.658][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.659][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.663][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:02:15.664][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:02:15.665][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.666][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.669][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:15.670][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:02:15.671][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.672][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.676][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:15.677][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:02:15.678][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.679][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.682][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:15.683][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:02:15.684][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.685][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.689][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:15.690][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:02:15.691][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.692][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.695][ef$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:02:15.696][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:02:15.697][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.698][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.702][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:02:15.703][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:02:15.704][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.705][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.708][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:02:15.709][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:02:15.710][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.711][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.715][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:02:15.716][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:02:15.717][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.718][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.721][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:15.722][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:02:15.723][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.724][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.728][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:15.729][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:02:15.730][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.731][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.734][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:15.735][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:15.736][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.737][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.741][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:15.742][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:02:15.743][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.744][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.751][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:15.752][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:15.753][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.754][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:15.757][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:02:15.758][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:02:15.759][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.760][ef$get] fields variable is a list.
biodb.INFO [2026-03-07 16:02:15.766][biodb::testThat]
biodb.INFO [2026-03-07 16:02:15.767][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-03-07 16:02:15.768][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:15.769][biodb::testThat]
biodb.DEBUG[2026-03-07 16:02:15.782][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-03-07 16:02:15.784][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-03-07 16:02:15.787][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-03-07 16:02:15.814][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-03-07 16:02:15.815][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-03-07 16:02:15.816][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-07 16:02:15.940][biodb::testThat]
biodb.INFO [2026-03-07 16:02:15.941][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-03-07 16:02:15.942][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:15.943][biodb::testThat]
biodb.TRACE[2026-03-07 16:02:15.946][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:15.947][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:15.947][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:15.948][ef$get] fields variable is a list.
biodb.DEBUG[2026-03-07 16:02:15.949][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2026-03-07 16:02:15.969][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-03-07 16:02:16.011][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-03-07 16:02:16.013][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-03-07 16:02:16.014][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-03-07 16:02:16.015][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-03-07 16:02:16.030][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-07 16:02:16.080][biodb::testThat]
biodb.INFO [2026-03-07 16:02:16.081][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-03-07 16:02:16.082][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:16.082][biodb::testThat]
biodb.DEBUG[2026-03-07 16:02:16.089][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-03-07 16:02:16.090][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-03-07 16:02:16.091][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-03-07 16:02:16.092][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-03-07 16:02:16.094][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-03-07 16:02:16.094][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-07 16:02:16.133][biodb::testThat]
biodb.INFO [2026-03-07 16:02:16.134][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-03-07 16:02:16.135][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:16.136][biodb::testThat]
biodb.DEBUG[2026-03-07 16:02:16.139][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-03-07 16:02:16.140][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-03-07 16:02:16.142][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-03-07 16:02:16.143][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-03-07 16:02:16.144][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-03-07 16:02:16.145][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-07 16:02:16.187][biodb::testThat]
biodb.INFO [2026-03-07 16:02:16.188][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-03-07 16:02:16.189][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:16.190][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-07 16:02:16.229][biodb::testThat]
biodb.INFO [2026-03-07 16:02:16.230][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-03-07 16:02:16.231][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:16.232][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-07 16:02:16.275][biodb::testThat]
biodb.INFO [2026-03-07 16:02:16.276][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-03-07 16:02:16.277][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:16.278][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-07 16:02:16.317][biodb::testThat]
biodb.INFO [2026-03-07 16:02:16.318][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-03-07 16:02:16.318][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:02:16.319][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2026-03-07 16:02:16.372][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:16.373][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:16.374][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:16.375][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:16.376][ef$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:02:16.377][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:02:16.378][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:16.379][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:16.380][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:16.381][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:16.381][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:16.382][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:16.383][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:02:16.384][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:02:16.385][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:16.386][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:16.387][ef$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:02:16.388][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:02:16.389][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:16.390][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:02:16.391][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:16.392][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:02:16.392][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:02:16.393][ef$get] fields variable is a list.
biodb.INFO [2026-03-07 16:02:16.394][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-07 16:02:16.395][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2026-03-07 16:02:16.396][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-07 16:02:16.397][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:02:16.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:02:16.399][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:02:16.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:02:16.400][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:02:16.401][FUN] Functions in observer 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 1 | PASS 103 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1):

══ 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 1 | PASS 103 ]
Error:
! Test failures.
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* 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 ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
* 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 loading without being on the library search path ... 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:
  ── 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 1 | PASS 103 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
  ‘/home/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 ‘1.16.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor ‘EntryMaker::EntryMaker()’:
EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/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 -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/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)