Back to Long Tests report for BioC 3.22

This page was generated on 2026-02-14 23:55 -0500 (Sat, 14 Feb 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4889
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4679
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 6/31HostnameOS / ArchCHECK
biodbHmdb 1.16.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-02-14 09:55 -0500 (Sat, 14 Feb 2026)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_22
git_last_commit: 4102973
git_last_commit_date: 2025-10-29 11:13:48 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on merida1

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

raw results


Summary

Package: biodbHmdb
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
StartedAt: 2026-02-14 16:01:16 -0500 (Sat, 14 Feb 2026)
EndedAt: 2026-02-14 16:02:48 -0500 (Sat, 14 Feb 2026)
EllapsedTime: 92.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2026-02-14 16:02:42.319][biodb::testContext]
biodb.INFO [2026-02-14 16:02:42.323][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-14 16:02:42.325][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-02-14 16:02:42.326][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-14 16:02:42.328][biodb::testContext]
biodb.INFO [2026-02-14 16:02:42.335][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-14 16:02:42.337][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-14 16:02:42.346][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-14 16:02:42.351][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-14 16:02:42.352][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-14 16:02:42.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.359][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-14 16:02:42.392][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-14 16:02:42.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.397][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-14 16:02:42.399][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-14 16:02:42.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.404][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-14 16:02:42.407][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-14 16:02:42.409][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-14 16:02:42.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.415][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-14 16:02:42.417][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-14 16:02:42.418][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-14 16:02:42.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.423][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-14 16:02:42.424][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-14 16:02:42.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.429][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-14 16:02:42.430][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-14 16:02:42.432][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-14 16:02:42.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.436][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-14 16:02:42.438][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-14 16:02:42.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.443][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-14 16:02:42.445][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-14 16:02:42.446][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-14 16:02:42.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.453][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-14 16:02:42.454][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-14 16:02:42.455][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-14 16:02:42.456][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-14 16:02:42.458][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-14 16:02:42.459][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-14 16:02:42.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.466][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-14 16:02:42.467][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-14 16:02:42.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.472][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-14 16:02:42.477][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-14 16:02:42.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.487][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-14 16:02:42.488][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-14 16:02:42.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.493][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-14 16:02:42.494][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-14 16:02:42.496][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-14 16:02:42.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.501][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-14 16:02:42.502][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-14 16:02:42.513][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-14 16:02:42.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.518][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-14 16:02:42.519][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-14 16:02:42.520][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-14 16:02:42.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.527][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-14 16:02:42.571][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:42.598][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-14 16:02:42.600][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:42.601][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:02:42.602][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:42.604][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:02:42.605][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:42.606][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:02:42.608][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-14 16:02:42.609][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:02:42.610][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:42.612][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-14 16:02:42.613][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:02:42.614][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:42.616][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:42.617][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-14 16:02:42.617][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-14 16:02:42.617][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-14 16:02:42.617][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-14 16:02:42.617][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-14 16:02:42.619][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:02:42.621][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:42.622][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:42.623][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:02:42.625][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:42.626][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:42.627][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:02:42.628][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:42.629][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:02:42.631][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:02:42.632][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:42.633][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:42.635][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-14 16:02:42.637][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:42.638][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-14 16:02:42.640][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:42.642][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:02:42.643][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:42.644][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:02:42.645][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:42.651][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:02:42.652][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-14 16:02:42.653][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:02:42.655][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:42.661][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-14 16:02:42.662][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:02:42.663][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:42.665][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:42.668][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-14 16:02:42.668][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-14 16:02:42.668][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-14 16:02:42.668][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-14 16:02:42.668][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-14 16:02:42.669][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:02:42.671][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:42.672][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:42.673][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:02:42.674][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:42.675][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:42.677][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:02:42.678][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:42.679][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:02:42.680][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:02:42.682][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:42.683][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:42.684][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-14 16:02:42.687][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:42.693][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-14 16:02:42.695][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:42.696][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:02:42.697][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:42.699][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:02:42.700][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:42.701][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:02:42.702][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-14 16:02:42.703][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:02:42.705][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:42.706][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-14 16:02:42.707][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:02:42.708][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:42.710][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:42.711][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:42.712][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:02:42.713][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:42.714][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:42.716][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:02:42.717][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:42.718][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:42.720][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:02:42.721][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:42.723][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:02:42.724][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:02:42.726][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:42.727][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:42.729][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-14 16:02:42.731][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:42.732][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-14 16:02:42.737][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:42.738][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:02:42.739][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:42.741][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:02:42.742][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:42.743][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:02:42.745][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-14 16:02:42.746][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:02:42.747][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:42.748][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-14 16:02:42.750][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:02:42.752][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:42.753][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:42.754][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:42.755][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:02:42.760][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:42.762][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:42.763][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:02:42.764][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:42.771][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:42.772][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:02:42.774][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:42.775][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:02:42.777][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:02:42.778][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:42.779][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:42.783][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-14 16:02:42.784][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:42.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:42.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:42.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:42.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:42.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:42.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:42.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:42.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:42.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:42.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.822][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[2026-02-14 16:02:42.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:42.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:42.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:42.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:42.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:42.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:42.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:42.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:42.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:42.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:42.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:42.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:42.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:42.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:42.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:42.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:42.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:42.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:42.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:42.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:42.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:42.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:42.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:42.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:42.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:42.918][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-14 16:02:42.923][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-14 16:02:42.925][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-14 16:02:42.927][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-14 16:02:42.928][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-14 16:02:42.930][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-14 16:02:42.932][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-14 16:02:42.934][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-14 16:02:42.935][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-14 16:02:42.937][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-14 16:02:42.939][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-14 16:02:42.941][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-14 16:02:42.942][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-14 16:02:42.944][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-14 16:02:42.946][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-14 16:02:42.947][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-14 16:02:42.949][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-14 16:02:42.951][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-14 16:02:42.953][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-14 16:02:42.955][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-14 16:02:42.957][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-14 16:02:42.958][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-14 16:02:42.960][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-14 16:02:42.962][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-14 16:02:42.964][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-14 16:02:42.966][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-14 16:02:42.967][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-14 16:02:42.970][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-14 16:02:42.972][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-14 16:02:42.974][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-14 16:02:42.975][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-14 16:02:42.977][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-14 16:02:42.979][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-14 16:02:42.983][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-14 16:02:42.985][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-14 16:02:42.987][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-14 16:02:42.993][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-14 16:02:42.995][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-14 16:02:42.996][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-14 16:02:42.998][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-14 16:02:43.003][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-14 16:02:43.005][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-14 16:02:43.007][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-14 16:02:43.010][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-14 16:02:43.012][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-14 16:02:43.013][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-14 16:02:43.015][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-14 16:02:43.017][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-14 16:02:43.019][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-14 16:02:43.020][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-14 16:02:43.022][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-14 16:02:43.024][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-14 16:02:43.026][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-14 16:02:43.032][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-14 16:02:43.035][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-14 16:02:43.037][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-14 16:02:43.039][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-14 16:02:43.041][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-14 16:02:43.043][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-14 16:02:43.044][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-14 16:02:43.046][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-14 16:02:43.048][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-14 16:02:43.050][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-14 16:02:43.052][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-14 16:02:43.053][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-14 16:02:43.055][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-14 16:02:43.058][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-14 16:02:43.060][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-14 16:02:43.062][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-14 16:02:43.065][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-14 16:02:43.068][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-14 16:02:43.071][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-14 16:02:43.073][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-14 16:02:43.075][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-14 16:02:43.077][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-14 16:02:43.080][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-14 16:02:43.083][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-14 16:02:43.084][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-14 16:02:43.086][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-14 16:02:43.088][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-14 16:02:43.091][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-14 16:02:43.093][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-14 16:02:43.095][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-14 16:02:43.104][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-14 16:02:43.108][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-14 16:02:43.113][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-14 16:02:43.114][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.117][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:43.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:43.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:43.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:43.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:43.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:43.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:43.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:43.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:43.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:43.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:43.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:43.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:43.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:43.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:43.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:43.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:43.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:43.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:43.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:43.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:43.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:43.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:43.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:43.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:43.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:43.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:43.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:43.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:43.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:43.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:43.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:43.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:43.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:43.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:43.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:43.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:43.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:43.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:43.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:43.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:43.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:43.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:43.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:43.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:43.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:43.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:43.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:43.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:43.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:43.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:43.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:43.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:43.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:43.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:43.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:43.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:43.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:43.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:43.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:43.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:43.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:43.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:43.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:43.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2026-02-14 16:02:43.280][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2026-02-14 16:02:43.293][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2026-02-14 16:02:43.311][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2026-02-14 16:02:43.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:43.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:43.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:43.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:43.322][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2026-02-14 16:02:43.335][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2026-02-14 16:02:43.337][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:43.339][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2026-02-14 16:02:43.340][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:43.341][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:02:43.342][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:43.344][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2026-02-14 16:02:43.345][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:43.346][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:02:43.347][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-14 16:02:43.349][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:02:43.350][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:43.351][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2026-02-14 16:02:43.354][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:02:43.355][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2026-02-14 16:02:43.355][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2026-02-14 16:02:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2026-02-14 16:02:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2026-02-14 16:02:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2026-02-14 16:02:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2026-02-14 16:02:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2026-02-14 16:02:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2026-02-14 16:02:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2026-02-14 16:02:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2026-02-14 16:02:43.355][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2026-02-14 16:02:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2026-02-14 16:02:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2026-02-14 16:02:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2026-02-14 16:02:43.355][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2026-02-14 16:02:43.355][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2026-02-14 16:02:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2026-02-14 16:02:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2026-02-14 16:02:43.358][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:43.360][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-14 16:02:43.360][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2026-02-14 16:02:43.360][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2026-02-14 16:02:43.361][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-14 16:02:43.364][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:43.365][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:43.367][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:02:43.369][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:43.370][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:43.371][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:02:43.372][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2026-02-14 16:02:43.372][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2026-02-14 16:02:43.374][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:02:43.375][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:02:43.376][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:43.377][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:43.385][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2026-02-14 16:02:43.387][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-14 16:02:43.390][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-14 16:02:43.392][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-14 16:02:43.394][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-14 16:02:43.419][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2026-02-14 16:02:43.435][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2026-02-14 16:02:43.445][biodb::testThat]
biodb.INFO [2026-02-14 16:02:43.447][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-14 16:02:43.448][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:02:43.449][biodb::testThat]
biodb.TRACE[2026-02-14 16:02:43.468][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2026-02-14 16:02:43.470][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2026-02-14 16:02:43.474][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2026-02-14 16:02:43.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-14 16:02:43.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:43.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:43.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:43.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:43.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:43.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-14 16:02:43.523][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:43.524][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:43.526][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.527][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:43.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:43.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.560][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:43.561][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:43.562][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.564][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.604][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:43.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:43.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.610][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-14 16:02:43.611][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-14 16:02:43.612][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.613][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.615][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-14 16:02:43.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-14 16:02:43.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.623][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:43.629][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:43.630][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.633][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.634][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:43.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:43.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.639][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-14 16:02:43.641][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-14 16:02:43.642][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.643][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.645][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-14 16:02:43.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-14 16:02:43.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.650][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:43.651][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:43.652][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.654][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:43.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:43.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.660][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:43.668][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:43.670][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.671][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.673][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:43.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:43.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.678][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:43.679][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:43.681][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.682][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.684][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:43.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:43.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.690][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:43.691][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:43.692][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.694][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.695][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:43.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:43.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.701][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:43.702][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:43.703][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.705][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.706][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:43.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:43.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.712][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:43.713][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:43.714][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.715][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.717][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:43.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:43.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.723][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:43.725][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:43.726][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.727][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.729][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:43.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:43.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.737][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:43.742][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:43.744][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.745][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:43.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:43.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.753][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:43.754][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:43.757][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.759][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:43.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:43.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.766][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:43.767][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:43.768][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.769][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:43.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:43.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.778][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-14 16:02:43.779][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-14 16:02:43.781][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.783][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.785][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-14 16:02:43.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-14 16:02:43.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.794][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-02-14 16:02:43.795][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-14 16:02:43.797][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.802][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.804][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-14 16:02:43.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-14 16:02:43.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.809][ef$get] Asked field names are: super.class.
biodb.TRACE[2026-02-14 16:02:43.810][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:43.812][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.813][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.814][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2026-02-14 16:02:43.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:43.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:43.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:43.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:43.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:43.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:43.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:43.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.902][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-14 16:02:43.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-14 16:02:43.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.908][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-14 16:02:43.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-14 16:02:43.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.913][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-14 16:02:43.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-14 16:02:43.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.918][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:43.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:43.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.925][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:43.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:43.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.934][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:43.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:43.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-14 16:02:43.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-14 16:02:43.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-14 16:02:43.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-14 16:02:43.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-14 16:02:43.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-14 16:02:43.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:43.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:43.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:43.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:43.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:43.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:43.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.978][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:43.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:43.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.986][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:43.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:43.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.991][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:43.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:43.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:43.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:43.997][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:43.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:43.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.002][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:44.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:44.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.007][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:44.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:44.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.015][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:44.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:44.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.025][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:44.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:44.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.030][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:44.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:44.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.039][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-14 16:02:44.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-14 16:02:44.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.044][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-14 16:02:44.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-14 16:02:44.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.049][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-14 16:02:44.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-14 16:02:44.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.055][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:44.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:44.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.063][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:44.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:44.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.076][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:44.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:44.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.082][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:44.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:44.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.087][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:44.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:44.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:44.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:44.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.098][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:44.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:44.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.107][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:44.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:44.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.117][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:44.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:44.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.124][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:44.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:44.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.129][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:44.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:44.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.134][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:44.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:44.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:44.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:44.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:44.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:44.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:44.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:44.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.162][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:44.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:44.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.167][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:44.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:44.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.172][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:44.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:44.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.181][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:44.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:44.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.187][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:44.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:44.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.192][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:44.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:44.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.198][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:44.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:44.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.203][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:44.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:44.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.209][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:44.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:44.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.215][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-14 16:02:44.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-14 16:02:44.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.226][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-14 16:02:44.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-14 16:02:44.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.231][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-14 16:02:44.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-14 16:02:44.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.236][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-02-14 16:02:44.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:44.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:44.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:44.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:44.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:44.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.255][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:44.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:44.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.261][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-02-14 16:02:44.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:44.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.296][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:44.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:44.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.301][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:44.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:44.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.307][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:44.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:44.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.312][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:44.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:44.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.317][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:44.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:44.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.325][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-14 16:02:44.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-14 16:02:44.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.373][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-14 16:02:44.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-14 16:02:44.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.384][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-14 16:02:44.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-14 16:02:44.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-14 16:02:44.428][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2026-02-14 16:02:44.431][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-14 16:02:44.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-14 16:02:44.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.439][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-14 16:02:44.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-14 16:02:44.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.450][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-14 16:02:44.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-14 16:02:44.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.455][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-14 16:02:44.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-14 16:02:44.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.518][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-14 16:02:44.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-14 16:02:44.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.573][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-14 16:02:44.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-14 16:02:44.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.578][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-14 16:02:44.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-14 16:02:44.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.583][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-14 16:02:44.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-14 16:02:44.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.648][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.650][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.651][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.652][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:44.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:44.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.688][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:44.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:44.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.694][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:44.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:44.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.699][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:44.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:44.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.704][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:44.706][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:44.707][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.708][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.709][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:44.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:44.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:44.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:44.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:44.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:44.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:44.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:44.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.778][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:44.779][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:44.784][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.785][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:44.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:44.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.810][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:44.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:44.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.816][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:44.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:44.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.821][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:44.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:44.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.833][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:44.834][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:44.835][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.836][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.838][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:44.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:44.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-14 16:02:44.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-14 16:02:44.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-14 16:02:44.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-14 16:02:44.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-14 16:02:44.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-14 16:02:44.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.883][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-14 16:02:44.884][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-14 16:02:44.885][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.887][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-14 16:02:44.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-14 16:02:44.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.910][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:44.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:44.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.916][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:44.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:44.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.921][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:44.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:44.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.926][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:44.928][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:44.929][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.930][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.931][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:44.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:44.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.948][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:44.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:44.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:44.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:44.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.963][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:44.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:44.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.968][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:44.970][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:44.971][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.972][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.973][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:44.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:44.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.990][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-14 16:02:44.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-14 16:02:44.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:44.995][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-14 16:02:44.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-14 16:02:44.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:44.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.000][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-14 16:02:45.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-14 16:02:45.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.005][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-14 16:02:45.007][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-14 16:02:45.008][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.009][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.011][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-14 16:02:45.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-14 16:02:45.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.036][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:45.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:45.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.046][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:45.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:45.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.055][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:45.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:45.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.060][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:45.062][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:45.063][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.064][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.065][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:45.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:45.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.082][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-14 16:02:45.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-14 16:02:45.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.088][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-14 16:02:45.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-14 16:02:45.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.093][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-14 16:02:45.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-14 16:02:45.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.098][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-14 16:02:45.100][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-14 16:02:45.101][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.102][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.104][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-14 16:02:45.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-14 16:02:45.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:45.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:45.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:45.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:45.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:45.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:45.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.148][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:45.149][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:45.156][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.158][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:45.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:45.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.190][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:45.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:45.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.195][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:45.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:45.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.200][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:45.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:45.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.205][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:45.207][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:45.208][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.209][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.210][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:45.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:45.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.231][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:45.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:45.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.239][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:45.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:45.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.244][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:45.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:45.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.249][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:45.250][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:45.251][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.252][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.254][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:45.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:45.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.273][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:45.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:45.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.279][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:45.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:45.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.284][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:45.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:45.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.289][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:45.290][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:45.292][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.293][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.294][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:45.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:45.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.315][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-14 16:02:45.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-14 16:02:45.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.320][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-14 16:02:45.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-14 16:02:45.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.334][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-14 16:02:45.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-14 16:02:45.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.340][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-02-14 16:02:45.341][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-14 16:02:45.342][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.343][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.344][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-14 16:02:45.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-14 16:02:45.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.360][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:45.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:45.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:45.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:45.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.370][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:45.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:45.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.375][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:45.376][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:45.377][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.379][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.380][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:45.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:45.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.396][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:45.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:45.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:45.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:45.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.407][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:45.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:45.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.412][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:45.413][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:45.414][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.416][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.417][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:45.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:45.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.437][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:45.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:45.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.442][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:45.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:45.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.447][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:45.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:45.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.452][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:45.454][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:45.455][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.456][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.457][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:45.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:45.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.495][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:45.496][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:45.498][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.499][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.506][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-14 16:02:45.508][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-14 16:02:45.509][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.510][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.519][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:45.520][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:45.522][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.523][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.532][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-14 16:02:45.537][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-14 16:02:45.538][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.540][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.548][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:45.550][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-14 16:02:45.551][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.552][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.559][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:45.560][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-14 16:02:45.561][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.562][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.569][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:45.570][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-14 16:02:45.571][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.577][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.605][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:45.607][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-14 16:02:45.608][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.610][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.616][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-14 16:02:45.618][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-14 16:02:45.619][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.620][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.631][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:45.633][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:45.634][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.635][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.645][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:45.650][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:45.653][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.654][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.661][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:45.662][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:45.663][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.664][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.671][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:45.672][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-14 16:02:45.673][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.674][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.681][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:45.683][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-14 16:02:45.684][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.685][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.695][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:45.697][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:45.698][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.699][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.715][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:45.717][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-14 16:02:45.718][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.719][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.726][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:45.728][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:45.729][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.730][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:45.737][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-02-14 16:02:45.739][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-14 16:02:45.740][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:45.741][ef$get] fields variable is a list.
biodb.INFO [2026-02-14 16:02:45.755][biodb::testThat]
biodb.INFO [2026-02-14 16:02:45.760][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-14 16:02:45.761][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:02:45.763][biodb::testThat]
biodb.DEBUG[2026-02-14 16:02:45.782][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-14 16:02:45.787][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-14 16:02:45.903][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-14 16:02:45.947][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-14 16:02:45.949][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-14 16:02:45.950][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-14 16:02:46.216][biodb::testThat]
biodb.INFO [2026-02-14 16:02:46.217][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-14 16:02:46.218][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:02:46.220][biodb::testThat]
biodb.TRACE[2026-02-14 16:02:46.224][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:46.226][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:46.227][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:46.229][ef$get] fields variable is a list.
biodb.DEBUG[2026-02-14 16:02:46.231][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2026-02-14 16:02:46.265][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-14 16:02:46.340][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-14 16:02:46.342][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-14 16:02:46.344][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-14 16:02:46.347][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-14 16:02:46.367][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-14 16:02:46.569][biodb::testThat]
biodb.INFO [2026-02-14 16:02:46.573][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-14 16:02:46.574][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:02:46.575][biodb::testThat]
biodb.DEBUG[2026-02-14 16:02:46.590][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-14 16:02:46.591][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-14 16:02:46.593][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-14 16:02:46.595][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-14 16:02:46.596][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-14 16:02:46.598][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-14 16:02:46.769][biodb::testThat]
biodb.INFO [2026-02-14 16:02:46.770][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-14 16:02:46.772][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:02:46.774][biodb::testThat]
biodb.DEBUG[2026-02-14 16:02:46.779][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-14 16:02:46.780][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-14 16:02:46.782][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-14 16:02:46.784][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-14 16:02:46.786][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-14 16:02:46.787][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-14 16:02:46.886][biodb::testThat]
biodb.INFO [2026-02-14 16:02:46.887][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-14 16:02:46.888][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:02:46.890][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-14 16:02:47.119][biodb::testThat]
biodb.INFO [2026-02-14 16:02:47.120][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-14 16:02:47.122][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:02:47.123][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-14 16:02:47.353][biodb::testThat]
biodb.INFO [2026-02-14 16:02:47.354][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-14 16:02:47.355][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:02:47.356][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-14 16:02:47.545][biodb::testThat]
biodb.INFO [2026-02-14 16:02:47.546][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-14 16:02:47.547][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:02:47.548][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2026-02-14 16:02:47.774][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:47.775][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:47.777][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:47.778][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:47.779][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-14 16:02:47.780][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-14 16:02:47.781][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:47.783][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:47.784][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:47.785][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:47.786][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:47.788][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:47.789][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:47.790][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:47.791][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:47.793][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:47.794][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-14 16:02:47.795][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-14 16:02:47.797][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:47.799][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:47.800][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:47.801][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-14 16:02:47.805][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:47.806][ef$get] fields variable is a list.
biodb.INFO [2026-02-14 16:02:47.807][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-14 16:02:47.809][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2026-02-14 16:02:47.814][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-14 16:02:47.816][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:47.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:47.819][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:47.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:47.821][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:47.822][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".
[ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]

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

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

[ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]
Error:
! Test failures.
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
   5.       └─base::vapply(id, fct, FUN.VALUE = "")
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  
  [ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

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

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.16.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c EntryMaker.cpp -o EntryMaker.o
EntryMaker.cpp:6:5: warning: field 'accession_tag' will be initialized after field 'closed' [-Wreorder-ctor]
    accession_tag("<accession>", "</accession>"),
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    closed(true)
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FileEntryMaker.cpp -o FileEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c TagDetector.cpp -o TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c XmlSplitter.cpp -o XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractXmlEntries.cpp -o extractXmlEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-TagDetector.cpp -o test-100-TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)