Back to Long Tests report for BioC 3.21

This page was generated on 2025-10-04 23:55 -0400 (Sat, 04 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4832
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4613
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 7/30HostnameOS / ArchCHECK
biodbHmdb 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-10-04 09:55 -0400 (Sat, 04 Oct 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_21
git_last_commit: a7f0a0f
git_last_commit_date: 2025-04-15 12:42:50 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on nebbiolo1

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: 1.14.0
Command: /home/biocbuild/bbs-3.21-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_1.14.0.tar.gz
StartedAt: 2025-10-04 16:01:50 -0400 (Sat, 04 Oct 2025)
EndedAt: 2025-10-04 16:02:57 -0400 (Sat, 04 Oct 2025)
EllapsedTime: 67.1 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)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-10-04 16:02:53.504][biodb::testContext]
biodb.INFO [2025-10-04 16:02:53.506][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:02:53.507][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-10-04 16:02:53.508][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:02:53.509][biodb::testContext]
biodb.INFO [2025-10-04 16:02:53.515][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.1.
biodb.DEBUG[2025-10-04 16:02:53.517][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-10-04 16:02:53.524][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:02:53.525][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-04 16:02:53.526][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-04 16:02:53.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.530][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-04 16:02:53.547][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-04 16:02:53.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.551][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-04 16:02:53.552][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-04 16:02:53.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.564][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-04 16:02:53.565][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-04 16:02:53.566][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-04 16:02:53.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.569][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-04 16:02:53.570][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-04 16:02:53.571][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-04 16:02:53.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.575][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-04 16:02:53.576][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-04 16:02:53.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.579][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-04 16:02:53.580][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-04 16:02:53.581][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-04 16:02:53.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.585][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-04 16:02:53.586][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-04 16:02:53.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.589][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-04 16:02:53.590][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-04 16:02:53.591][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-04 16:02:53.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.594][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:02:53.595][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-04 16:02:53.596][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-04 16:02:53.597][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-04 16:02:53.598][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-04 16:02:53.599][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-04 16:02:53.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.603][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-04 16:02:53.604][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-04 16:02:53.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.607][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-04 16:02:53.608][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-04 16:02:53.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.612][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-04 16:02:53.613][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-04 16:02:53.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.616][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-04 16:02:53.617][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-04 16:02:53.618][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-04 16:02:53.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.621][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:02:53.622][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-04 16:02:53.626][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-04 16:02:53.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.630][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-04 16:02:53.631][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-04 16:02:53.632][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-04 16:02:53.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.637][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-04 16:02:53.669][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:53.683][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-04 16:02:53.684][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:53.685][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:53.686][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:53.687][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:53.688][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:53.689][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:53.690][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:02:53.691][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:53.692][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:53.693][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-04 16:02:53.694][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:53.695][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:53.696][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:53.697][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:53.697][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:02:53.697][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:02:53.697][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:02:53.697][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:02:53.698][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:53.698][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:53.699][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:53.700][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:53.701][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:53.702][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:53.703][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:53.704][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:53.705][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:53.706][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:53.706][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:53.707][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:53.709][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-04 16:02:53.710][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:53.711][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:02:53.712][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:53.713][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:53.714][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:53.715][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:53.716][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:53.721][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:53.722][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:02:53.723][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:53.724][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:53.725][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-04 16:02:53.726][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:53.727][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:53.728][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:53.729][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:53.729][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:02:53.729][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:02:53.729][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:02:53.729][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:02:53.730][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:53.731][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:53.732][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:53.732][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:53.733][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:53.734][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:53.735][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:53.736][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:53.737][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:53.738][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:53.739][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:53.740][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:53.741][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-04 16:02:53.742][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:53.743][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-04 16:02:53.744][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:53.745][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:53.746][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:53.747][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:53.748][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:53.749][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:53.750][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:02:53.751][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:53.752][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:53.753][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-04 16:02:53.754][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:53.755][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:53.756][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:53.757][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:53.758][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:53.758][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:53.759][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:53.760][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:53.761][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:53.762][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:53.763][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:53.764][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:53.765][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:53.765][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:53.766][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:53.767][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:53.768][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-04 16:02:53.770][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:53.771][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:02:53.772][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:53.773][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:53.774][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:53.775][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:53.776][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:53.777][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:53.778][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:02:53.778][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:53.779][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:53.780][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-04 16:02:53.781][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:53.782][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:53.783][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:53.784][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:53.785][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:53.786][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:53.787][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:53.788][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:53.789][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:53.789][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:53.790][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:53.791][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:53.792][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:53.793][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:53.794][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:53.795][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:53.799][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:02:53.799][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:53.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:53.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:53.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:53.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:53.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:53.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:53.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:53.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:53.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:53.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:53.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:53.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:53.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:53.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:53.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:53.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:53.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:53.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:53.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:53.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.843][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[2025-10-04 16:02:53.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:53.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:53.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:53.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:53.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:53.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:53.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:53.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:53.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:53.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:53.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:53.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:53.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:53.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:53.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:53.868][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[2025-10-04 16:02:53.869][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-04 16:02:53.873][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-04 16:02:53.875][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-04 16:02:53.899][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-04 16:02:53.901][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-04 16:02:53.902][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-04 16:02:53.904][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-04 16:02:53.906][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-04 16:02:53.907][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-04 16:02:53.909][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-04 16:02:53.910][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-04 16:02:53.912][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-04 16:02:53.913][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-04 16:02:53.915][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-04 16:02:53.916][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-04 16:02:53.918][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-04 16:02:53.919][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-04 16:02:53.921][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-04 16:02:53.923][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-04 16:02:53.924][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-04 16:02:53.926][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-04 16:02:53.927][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-04 16:02:53.928][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-04 16:02:53.930][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-04 16:02:53.931][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-04 16:02:53.933][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-04 16:02:53.934][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-04 16:02:53.936][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-04 16:02:53.937][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-04 16:02:53.939][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-04 16:02:53.940][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-04 16:02:53.942][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-04 16:02:53.943][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-04 16:02:53.944][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-04 16:02:53.946][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-04 16:02:53.947][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-04 16:02:53.949][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-04 16:02:53.950][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-04 16:02:53.952][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-04 16:02:53.953][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-04 16:02:53.955][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-04 16:02:53.956][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-04 16:02:53.957][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-04 16:02:53.959][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-04 16:02:53.960][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-04 16:02:53.962][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-04 16:02:53.963][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-04 16:02:53.965][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-04 16:02:53.966][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-04 16:02:53.968][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-04 16:02:53.969][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-04 16:02:53.970][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-04 16:02:53.972][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-04 16:02:53.973][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-04 16:02:53.975][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-04 16:02:53.976][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-04 16:02:53.978][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-04 16:02:53.979][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-04 16:02:53.981][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-04 16:02:53.982][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-04 16:02:53.983][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-04 16:02:53.985][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-04 16:02:53.986][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-04 16:02:53.988][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-04 16:02:53.989][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-04 16:02:53.991][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-04 16:02:53.992][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-04 16:02:53.994][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-04 16:02:53.995][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-04 16:02:53.997][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-04 16:02:53.998][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-04 16:02:53.999][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-04 16:02:54.001][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-04 16:02:54.002][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-04 16:02:54.004][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-04 16:02:54.005][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-04 16:02:54.006][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-04 16:02:54.008][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-04 16:02:54.009][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-04 16:02:54.011][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-04 16:02:54.012][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-04 16:02:54.014][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-04 16:02:54.015][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-04 16:02:54.022][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-04 16:02:54.024][initialize] This is biodb version 1.16.1.
biodb.DEBUG[2025-10-04 16:02:54.027][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:02:54.028][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.030][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:54.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:54.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:54.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:54.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:54.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:54.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:54.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:54.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:54.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:54.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:54.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:54.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:54.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:54.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:54.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:54.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:54.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:54.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:54.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:54.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:54.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:54.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:54.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:54.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:54.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:54.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:54.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:54.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:54.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:54.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:54.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:54.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:54.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:54.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:54.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:54.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:54.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:54.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:54.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:54.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:54.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:54.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:54.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:54.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:54.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:54.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:54.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:54.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.116][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[2025-10-04 16:02:54.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:54.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:54.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:54.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:54.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:54.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:54.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:54.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:54.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:54.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:54.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:54.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:54.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:54.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:54.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:54.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2025-10-04 16:02:54.140][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-10-04 16:02:54.150][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-10-04 16:02:54.163][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-10-04 16:02:54.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:54.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:54.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:54.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:54.170][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-10-04 16:02:54.179][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-10-04 16:02:54.181][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:54.182][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-10-04 16:02:54.183][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:54.184][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:54.185][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:54.186][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-10-04 16:02:54.187][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:54.188][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:54.188][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-04 16:02:54.189][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:54.190][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:54.191][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-10-04 16:02:54.192][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:54.193][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-10-04 16:02:54.193][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-10-04 16:02:54.193][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-10-04 16:02:54.193][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-10-04 16:02:54.193][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-10-04 16:02:54.193][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-10-04 16:02:54.193][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-10-04 16:02:54.193][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-10-04 16:02:54.193][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-10-04 16:02:54.193][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-10-04 16:02:54.193][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-10-04 16:02:54.193][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-10-04 16:02:54.193][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-10-04 16:02:54.193][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-10-04 16:02:54.193][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-10-04 16:02:54.193][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-10-04 16:02:54.193][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-10-04 16:02:54.193][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-10-04 16:02:54.194][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:54.195][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:54.195][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-10-04 16:02:54.195][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-10-04 16:02:54.196][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-04 16:02:54.197][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:54.198][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:54.199][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:54.200][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:54.201][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:54.202][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:54.203][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-10-04 16:02:54.203][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-10-04 16:02:54.204][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:54.204][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:54.205][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:54.206][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:54.212][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-10-04 16:02:54.213][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-04 16:02:54.219][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-04 16:02:54.220][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-04 16:02:54.221][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-04 16:02:54.243][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-10-04 16:02:54.257][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-10-04 16:02:54.265][biodb::testThat]
biodb.INFO [2025-10-04 16:02:54.266][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-04 16:02:54.267][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:54.267][biodb::testThat]
biodb.TRACE[2025-10-04 16:02:54.271][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-10-04 16:02:54.273][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-10-04 16:02:54.276][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-10-04 16:02:54.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-04 16:02:54.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:54.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:54.298][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:54.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:54.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:54.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-04 16:02:54.311][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.312][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.314][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.331][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.332][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.334][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.358][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.362][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:54.363][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:54.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.364][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.366][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:54.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:54.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.370][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:54.371][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:54.372][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.372][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.374][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:54.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:54.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.378][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:54.379][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:54.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.380][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:54.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:54.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.394][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:54.395][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:54.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.397][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.398][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:54.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:54.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.402][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:54.403][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:54.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.405][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.406][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:54.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:54.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.410][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:54.411][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:54.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.413][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.414][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:54.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:54.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.418][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:54.419][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:54.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.420][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.422][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:54.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:54.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.425][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:54.426][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:54.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.428][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.429][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:54.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:54.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.433][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:54.434][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:54.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.436][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.437][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:54.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:54.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.441][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:54.442][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:54.443][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.444][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.445][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:54.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:54.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.449][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:54.450][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:54.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.452][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.453][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:54.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:54.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.457][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:54.458][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:54.459][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.459][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:54.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:54.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.464][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:54.465][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:54.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.467][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.468][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:54.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:54.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.472][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:54.473][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:54.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.475][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.476][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:54.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:54.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.480][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:54.481][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:54.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.483][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.484][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:54.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:54.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.488][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-10-04 16:02:54.489][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:54.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.490][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.492][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-10-04 16:02:54.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:54.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.579][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:54.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:54.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.583][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:54.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:54.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.587][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:54.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:54.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.590][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:54.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:54.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.594][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:54.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:54.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.598][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:54.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:54.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:54.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:54.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:54.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:54.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:54.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:54.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:54.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:54.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.617][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:54.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:54.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:54.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:54.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.625][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:54.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:54.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.628][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:54.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:54.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.632][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:54.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:54.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.636][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:54.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:54.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.640][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:54.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:54.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.644][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:54.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:54.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.647][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:54.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:54.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.651][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:54.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:54.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.655][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:54.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:54.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.659][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:54.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:54.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.666][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:54.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:54.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.670][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:54.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:54.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.673][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:54.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:54.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.677][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:54.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:54.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.681][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:54.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:54.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.685][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:54.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:54.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.689][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:54.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:54.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.692][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:54.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:54.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.696][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:54.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:54.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.700][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:54.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:54.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.704][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:54.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:54.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.708][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:54.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:54.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.711][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:54.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:54.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.715][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:54.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:54.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:54.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:54.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:54.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:54.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:54.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:54.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.730][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:54.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:54.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:54.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:54.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.738][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:54.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:54.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.742][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:54.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:54.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.745][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:54.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:54.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.749][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:54.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:54.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.753][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.757][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.761][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.764][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:54.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:54.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.768][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:54.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:54.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.772][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:54.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:54.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.776][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-10-04 16:02:54.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:54.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.779][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:54.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:54.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:54.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:54.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.790][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:54.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:54.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.794][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-10-04 16:02:54.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:54.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:54.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:54.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.818][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:54.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:54.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.822][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:54.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:54.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.826][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:54.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:54.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.830][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:54.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:54.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.834][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:54.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:54.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.837][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:54.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:54.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.845][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:54.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:54.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-04 16:02:54.872][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-10-04 16:02:54.874][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:02:54.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:02:54.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.878][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:02:54.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:02:54.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.882][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-04 16:02:54.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-04 16:02:54.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.885][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-04 16:02:54.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-04 16:02:54.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.898][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:54.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:54.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.933][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:54.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:54.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.937][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:54.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:54.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.941][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:54.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:54.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.962][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.963][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.965][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:54.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:54.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.977][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.981][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.985][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.988][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.990][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.991][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:54.992][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:54.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:54.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:55.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:55.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:55.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:55.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:55.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:55.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.014][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:55.015][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:55.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.016][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:55.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:55.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.031][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:55.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:55.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.035][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:55.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:55.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.039][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:55.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:55.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.042][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:55.043][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:55.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.045][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.046][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:55.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:55.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:55.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:55.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.060][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:55.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:55.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:55.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:55.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.067][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:55.068][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:55.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.070][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:55.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:55.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.081][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:55.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:55.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.085][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:55.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:55.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.089][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:55.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:55.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.092][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:55.093][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:55.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.095][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.096][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:55.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:55.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.106][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:55.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:55.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.110][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:55.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:55.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:55.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:55.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.117][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:55.118][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:55.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.120][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.121][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:55.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:55.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.131][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:55.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:55.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.134][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:55.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:55.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.138][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:55.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:55.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.146][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:55.147][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:55.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.149][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.150][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:55.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:55.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.160][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:55.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:55.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.164][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:55.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:55.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.167][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:55.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:55.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.171][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:55.172][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:55.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.174][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.175][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:55.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:55.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.185][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:55.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:55.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.189][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:55.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:55.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.192][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:55.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:55.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.196][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:55.197][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:55.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.199][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.200][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:55.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:55.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:55.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:55.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.214][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:55.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:55.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:55.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:55.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.221][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:55.222][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:55.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.224][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:55.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:55.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.235][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:55.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:55.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.238][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:55.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:55.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.242][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:55.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:55.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.246][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:55.247][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:55.248][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.249][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.250][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:55.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:55.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.263][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:55.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:55.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.267][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:55.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:55.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.271][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:55.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:55.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.274][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:55.275][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:55.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.277][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.278][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:55.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:55.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.288][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:55.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:55.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.292][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:55.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:55.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.296][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:55.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:55.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.300][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:55.301][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:55.301][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.302][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.303][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:55.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:55.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.313][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:55.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:55.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.317][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:55.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:55.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.321][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:55.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:55.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.325][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:55.326][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:55.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.328][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.329][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:55.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:55.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.339][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:55.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:55.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.342][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:55.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:55.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.346][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:55.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:55.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.350][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:55.351][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:55.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.353][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:55.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:55.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.364][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:55.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:55.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.368][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:55.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:55.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:55.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:55.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.375][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:55.377][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:55.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.382][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.383][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:55.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:55.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.394][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:55.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:55.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.398][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:55.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:55.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.402][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:55.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:55.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.406][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:55.407][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:55.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.409][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.410][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:55.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:55.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.420][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:55.421][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:55.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.423][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.427][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:55.428][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:55.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.430][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.433][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:55.434][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:55.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.436][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.440][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:55.441][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:55.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.443][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.447][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:55.448][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:55.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.449][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.453][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:55.454][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:55.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.456][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.460][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:55.461][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:55.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.463][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.466][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:55.467][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:55.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.469][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.473][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:55.474][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:55.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.476][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.480][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:55.481][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:55.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.483][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.486][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:55.487][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:55.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.489][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.493][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:55.494][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:55.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.499][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.503][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:55.504][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:55.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.506][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.510][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:55.511][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:55.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.512][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.516][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:55.517][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:55.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.519][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.523][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:55.524][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:55.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.526][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.529][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:55.530][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:55.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.532][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.536][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:55.537][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:55.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.539][ef$get] fields variable is a list.
biodb.INFO [2025-10-04 16:02:55.545][biodb::testThat]
biodb.INFO [2025-10-04 16:02:55.546][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-04 16:02:55.547][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:55.548][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:55.561][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-04 16:02:55.562][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-04 16:02:55.565][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-04 16:02:55.592][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-04 16:02:55.593][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-04 16:02:55.594][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-04 16:02:55.633][biodb::testThat]
biodb.INFO [2025-10-04 16:02:55.634][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-04 16:02:55.635][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:55.636][biodb::testThat]
biodb.TRACE[2025-10-04 16:02:55.639][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:55.640][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:55.641][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.642][ef$get] fields variable is a list.
biodb.DEBUG[2025-10-04 16:02:55.643][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-10-04 16:02:55.662][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-04 16:02:55.710][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-04 16:02:55.711][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-04 16:02:55.713][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-04 16:02:55.714][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-04 16:02:55.726][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-04 16:02:55.748][biodb::testThat]
biodb.INFO [2025-10-04 16:02:55.749][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-04 16:02:55.750][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:55.751][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:55.757][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-04 16:02:55.758][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-04 16:02:55.760][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-04 16:02:55.761][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-04 16:02:55.762][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-04 16:02:55.763][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-04 16:02:55.775][biodb::testThat]
biodb.INFO [2025-10-04 16:02:55.776][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-04 16:02:55.777][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:55.777][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:55.781][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-04 16:02:55.782][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-04 16:02:55.783][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-04 16:02:55.784][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-04 16:02:55.785][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-04 16:02:55.786][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-04 16:02:55.798][biodb::testThat]
biodb.INFO [2025-10-04 16:02:55.799][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-04 16:02:55.800][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:55.801][biodb::testThat]
biodb.INFO [2025-10-04 16:02:55.817][biodb::testThat]
biodb.INFO [2025-10-04 16:02:55.818][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-04 16:02:55.819][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:55.819][biodb::testThat]
biodb.INFO [2025-10-04 16:02:55.832][biodb::testThat]
biodb.INFO [2025-10-04 16:02:55.833][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-04 16:02:55.834][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:55.835][biodb::testThat]
biodb.INFO [2025-10-04 16:02:55.847][biodb::testThat]
biodb.INFO [2025-10-04 16:02:55.848][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-04 16:02:55.849][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:55.850][biodb::testThat]
biodb.TRACE[2025-10-04 16:02:55.874][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:55.875][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:55.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.877][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.878][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:55.879][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:55.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.881][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.882][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:55.883][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:55.883][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.884][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.885][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:55.886][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:55.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.888][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.889][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:55.890][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:55.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.892][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:55.893][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:55.894][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:55.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:55.896][ef$get] fields variable is a list.
biodb.INFO [2025-10-04 16:02:55.897][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-04 16:02:55.898][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-10-04 16:02:55.899][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-04 16:02:55.899][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:55.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:55.901][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:55.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:55.903][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:55.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]

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

[ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘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-3.21-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 ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
   5.       └─base::vapply(id, fct, FUN.VALUE = "")
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  
  [ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log’
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.14.0’
** 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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-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-3.21-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-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)