Back to Long Tests report for BioC 3.21

This page was generated on 2025-09-20 23:55 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 7/30HostnameOS / ArchCHECK
biodbHmdb 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-09-20 09:55 -0400 (Sat, 20 Sep 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_21
git_last_commit: a7f0a0f
git_last_commit_date: 2025-04-15 12:42:50 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  WARNINGS  
merida1macOS 12.7.5 Monterey / x86_64  WARNINGS  

CHECK results for biodbHmdb on nebbiolo1

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

raw results


Summary

Package: biodbHmdb
Version: 1.14.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.14.0.tar.gz
StartedAt: 2025-09-20 16:02:03 -0400 (Sat, 20 Sep 2025)
EndedAt: 2025-09-20 16:03:15 -0400 (Sat, 20 Sep 2025)
EllapsedTime: 72.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: biodbHmdb.Rcheck
Warnings: 2

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-09-20 16:03:10.589][biodb::testContext]
biodb.INFO [2025-09-20 16:03:10.591][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-20 16:03:10.592][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-09-20 16:03:10.593][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-20 16:03:10.594][biodb::testContext]
biodb.INFO [2025-09-20 16:03:10.600][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-09-20 16:03:10.602][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-09-20 16:03:10.609][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-20 16:03:10.610][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-20 16:03:10.612][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-20 16:03:10.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.615][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-20 16:03:10.634][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-20 16:03:10.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.637][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-20 16:03:10.638][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-20 16:03:10.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.642][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-20 16:03:10.643][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-20 16:03:10.644][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-20 16:03:10.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.648][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-20 16:03:10.649][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-20 16:03:10.650][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-20 16:03:10.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.654][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-20 16:03:10.655][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-20 16:03:10.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.659][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-20 16:03:10.660][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-20 16:03:10.661][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-20 16:03:10.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.665][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-20 16:03:10.666][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-20 16:03:10.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.669][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-20 16:03:10.671][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-20 16:03:10.672][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-20 16:03:10.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.675][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-20 16:03:10.676][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-20 16:03:10.677][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-20 16:03:10.678][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-20 16:03:10.680][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-20 16:03:10.681][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-20 16:03:10.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.684][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-20 16:03:10.685][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-20 16:03:10.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.689][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-20 16:03:10.690][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-20 16:03:10.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.694][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-20 16:03:10.695][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-20 16:03:10.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.699][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-20 16:03:10.700][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-09-20 16:03:10.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.704][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-20 16:03:10.705][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-20 16:03:10.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.709][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-20 16:03:10.710][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-20 16:03:10.714][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-20 16:03:10.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.718][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-20 16:03:10.719][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-20 16:03:10.720][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-20 16:03:10.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.726][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-20 16:03:10.766][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:10.792][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-09-20 16:03:10.794][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:10.795][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:03:10.796][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:10.797][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-20 16:03:10.798][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:10.800][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:03:10.801][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-20 16:03:10.802][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:03:10.803][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:10.805][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-20 16:03:10.806][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:03:10.807][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:10.809][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:10.810][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-20 16:03:10.810][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-20 16:03:10.810][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-20 16:03:10.810][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-20 16:03:10.810][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-20 16:03:10.811][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-20 16:03:10.812][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:10.813][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:10.814][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:03:10.815][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:10.816][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:10.817][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:03:10.819][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:10.820][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:03:10.821][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:03:10.822][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:10.823][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:10.824][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-20 16:03:10.827][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:10.828][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-20 16:03:10.829][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:10.830][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:03:10.831][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:10.833][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-20 16:03:10.834][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:10.835][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:03:10.836][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-20 16:03:10.837][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:03:10.838][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:10.839][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-20 16:03:10.841][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:03:10.842][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:10.843][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:10.844][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-20 16:03:10.844][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-20 16:03:10.844][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-20 16:03:10.844][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-20 16:03:10.844][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-20 16:03:10.845][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-20 16:03:10.846][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:10.847][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:10.849][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:03:10.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:10.851][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:10.852][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:03:10.853][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:10.854][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:03:10.855][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:03:10.856][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:10.857][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:10.859][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-20 16:03:10.861][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:10.862][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-09-20 16:03:10.863][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:10.864][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:03:10.865][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:10.866][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-20 16:03:10.868][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:10.869][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:03:10.870][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-20 16:03:10.871][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:03:10.872][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:10.873][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-20 16:03:10.874][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:03:10.876][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:10.877][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:10.878][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:10.879][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-20 16:03:10.880][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:10.881][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:10.882][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:03:10.883][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:10.884][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:10.885][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:03:10.887][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:10.888][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:03:10.889][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:03:10.890][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:10.891][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:10.892][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-20 16:03:10.894][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:10.896][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-20 16:03:10.897][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:10.898][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:03:10.899][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:10.900][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-20 16:03:10.901][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:10.903][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:03:10.904][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-20 16:03:10.905][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:03:10.906][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:10.907][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-20 16:03:10.908][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:03:10.910][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:10.911][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:10.912][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:10.913][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-20 16:03:10.914][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:10.915][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:10.916][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:03:10.917][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:10.918][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:10.920][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:03:10.921][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:10.922][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:03:10.923][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:03:10.924][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:10.925][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:10.930][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-20 16:03:10.931][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:10.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:10.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:10.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:10.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:10.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:10.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:10.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:10.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:10.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:10.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:10.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:10.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:10.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:10.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:10.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:10.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:10.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:10.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:10.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:10.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:10.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:10.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:10.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:10.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:10.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.028][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-20 16:03:11.033][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-20 16:03:11.035][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-20 16:03:11.036][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-20 16:03:11.037][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-20 16:03:11.039][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-20 16:03:11.040][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-20 16:03:11.042][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-20 16:03:11.043][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-20 16:03:11.045][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-20 16:03:11.046][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-20 16:03:11.048][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-20 16:03:11.049][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-20 16:03:11.050][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-20 16:03:11.052][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-20 16:03:11.053][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-20 16:03:11.055][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-20 16:03:11.056][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-20 16:03:11.058][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-20 16:03:11.059][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-20 16:03:11.061][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-20 16:03:11.062][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-20 16:03:11.063][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-20 16:03:11.065][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-20 16:03:11.066][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-20 16:03:11.068][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-20 16:03:11.069][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-20 16:03:11.071][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-20 16:03:11.072][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-20 16:03:11.073][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-20 16:03:11.075][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-20 16:03:11.076][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-20 16:03:11.078][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-20 16:03:11.079][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-20 16:03:11.081][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-20 16:03:11.082][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-20 16:03:11.083][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-20 16:03:11.085][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-20 16:03:11.086][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-20 16:03:11.088][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-20 16:03:11.089][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-20 16:03:11.091][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-20 16:03:11.092][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-20 16:03:11.094][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-20 16:03:11.095][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-20 16:03:11.096][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-20 16:03:11.098][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-20 16:03:11.099][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-20 16:03:11.101][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-20 16:03:11.102][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-20 16:03:11.104][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-20 16:03:11.105][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-20 16:03:11.107][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-20 16:03:11.108][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-20 16:03:11.109][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-20 16:03:11.111][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-20 16:03:11.112][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-20 16:03:11.114][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-20 16:03:11.115][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-20 16:03:11.117][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-20 16:03:11.118][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-20 16:03:11.120][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-20 16:03:11.121][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-20 16:03:11.122][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-20 16:03:11.124][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-20 16:03:11.125][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-20 16:03:11.127][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-20 16:03:11.128][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-20 16:03:11.130][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-20 16:03:11.131][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-20 16:03:11.132][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-20 16:03:11.134][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-20 16:03:11.135][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-20 16:03:11.137][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-20 16:03:11.138][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-20 16:03:11.140][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-20 16:03:11.141][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-20 16:03:11.143][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-20 16:03:11.144][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-20 16:03:11.145][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-20 16:03:11.147][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-20 16:03:11.148][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-20 16:03:11.150][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-20 16:03:11.156][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-20 16:03:11.158][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-09-20 16:03:11.161][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-20 16:03:11.162][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.164][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.279][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.DEBUG[2025-09-20 16:03:11.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.287][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-09-20 16:03:11.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:11.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:11.295][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-09-20 16:03:11.305][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-09-20 16:03:11.307][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:11.309][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-09-20 16:03:11.310][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:11.311][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:03:11.312][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:11.313][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-09-20 16:03:11.314][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:11.315][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:03:11.316][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-20 16:03:11.317][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:03:11.318][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:11.319][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-09-20 16:03:11.320][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:03:11.321][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-09-20 16:03:11.321][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-09-20 16:03:11.321][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-09-20 16:03:11.321][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-09-20 16:03:11.321][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-09-20 16:03:11.321][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-09-20 16:03:11.321][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-09-20 16:03:11.321][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-09-20 16:03:11.321][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-09-20 16:03:11.321][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-09-20 16:03:11.321][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-09-20 16:03:11.321][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-09-20 16:03:11.321][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-09-20 16:03:11.321][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-09-20 16:03:11.321][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-09-20 16:03:11.321][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-09-20 16:03:11.321][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-09-20 16:03:11.321][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-09-20 16:03:11.323][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:11.324][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-20 16:03:11.324][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-09-20 16:03:11.324][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-09-20 16:03:11.325][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-20 16:03:11.326][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:11.327][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:11.328][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:03:11.329][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:11.330][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:11.331][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:03:11.332][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-09-20 16:03:11.332][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-09-20 16:03:11.333][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:03:11.334][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:03:11.335][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:11.336][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:11.342][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-09-20 16:03:11.344][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-20 16:03:11.345][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-20 16:03:11.347][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-20 16:03:11.349][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-20 16:03:11.407][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-09-20 16:03:11.408][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-09-20 16:03:11.412][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-09-20 16:03:11.416][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-09-20 16:03:11.420][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-20 16:03:11.421][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-20 16:03:11.422][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-09-20 16:03:11.423][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-09-20 16:03:11.432][biodb::testThat]
biodb.INFO [2025-09-20 16:03:11.433][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-09-20 16:03:11.434][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:03:11.435][biodb::testThat]
biodb.TRACE[2025-09-20 16:03:11.439][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-09-20 16:03:11.441][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-09-20 16:03:11.444][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-09-20 16:03:11.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-20 16:03:11.453][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:11.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:11.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:11.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:11.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:11.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-20 16:03:11.481][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:11.482][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:11.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.484][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:11.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:11.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.503][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:11.504][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:11.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.506][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.533][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:11.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:11.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.537][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:03:11.538][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:03:11.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.540][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.541][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:03:11.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:03:11.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.546][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:11.547][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:11.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.549][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.550][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:11.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:11.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.555][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:03:11.556][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:03:11.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.558][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:03:11.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:03:11.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.563][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:11.564][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:11.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.566][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:11.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:11.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.572][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:11.573][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:11.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.575][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.576][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:11.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:11.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.581][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:11.582][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:11.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.595][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.596][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:11.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:11.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.601][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:11.602][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:11.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.604][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.605][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:11.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:11.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.609][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:11.610][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:11.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.612][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.613][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:11.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:11.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.618][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:11.619][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:11.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.621][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.622][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:11.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:11.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.626][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:11.627][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:11.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.629][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.630][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:11.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:11.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.635][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:11.636][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:11.637][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.638][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.639][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:11.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:11.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.643][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:11.644][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:11.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.646][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:11.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:11.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.652][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:11.653][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:11.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.655][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.656][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:11.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:11.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.660][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:11.662][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:11.662][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.663][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.665][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:11.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:11.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.669][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:03:11.670][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:03:11.671][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.672][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.673][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:03:11.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:03:11.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.677][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-09-20 16:03:11.679][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:11.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.681][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.682][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-09-20 16:03:11.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:11.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:11.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:11.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:11.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:11.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:11.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:11.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.731][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:03:11.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:03:11.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.736][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:03:11.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:03:11.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.745][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:03:11.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:03:11.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.749][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:11.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:11.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.753][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:11.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:11.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.757][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:11.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:11.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:03:11.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:03:11.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:03:11.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:03:11.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:03:11.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:03:11.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.774][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:11.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:11.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:11.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:11.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.782][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:11.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:11.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.786][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:11.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:11.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.790][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:11.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:11.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.794][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:11.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:11.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.799][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:11.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:11.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.803][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:11.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:11.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.807][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:11.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:11.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.811][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:11.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:11.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.815][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:11.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:11.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.819][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:11.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:11.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.824][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:11.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:11.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.828][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:11.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:11.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.832][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:11.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:11.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.836][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:11.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:11.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.840][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:11.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:11.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.844][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:11.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:11.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.849][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:11.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:11.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.853][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:11.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:11.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.857][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:11.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:11.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.861][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:11.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:11.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.865][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:11.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:11.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.869][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:11.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:11.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.873][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:11.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:11.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.878][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:11.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:11.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.882][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:11.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:11.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:11.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:11.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:11.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:11.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:11.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:11.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.903][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:11.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:11.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.907][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:11.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:11.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.911][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:11.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:11.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.915][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:11.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:11.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.919][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:11.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:11.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.924][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:11.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:11.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.928][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:11.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:11.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.932][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:11.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:11.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.936][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:11.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:11.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.940][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:03:11.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:03:11.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.945][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:03:11.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:03:11.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.949][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:03:11.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:03:11.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.953][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-09-20 16:03:11.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:11.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:11.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:11.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.961][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:11.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:11.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.965][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:11.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:11.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.969][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-09-20 16:03:11.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:11.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.992][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:11.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:11.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:11.996][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:11.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:11.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:11.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.000][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:12.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:12.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.004][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:12.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:12.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.009][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:12.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:12.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.013][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:12.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:12.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.017][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:12.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:12.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.025][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:12.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:12.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-20 16:03:12.059][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-09-20 16:03:12.062][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-20 16:03:12.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-20 16:03:12.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.066][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-20 16:03:12.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-20 16:03:12.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.070][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-20 16:03:12.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-20 16:03:12.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.075][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-20 16:03:12.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-20 16:03:12.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.112][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:12.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:12.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.147][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:12.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:12.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.151][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:12.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:12.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.155][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:12.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:12.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.179][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.180][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.182][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.194][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:12.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:12.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.199][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:12.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:12.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.203][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:12.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:12.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.213][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:12.214][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:12.215][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.216][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.217][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:12.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:12.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:12.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:12.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:12.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:12.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:12.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:12.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.240][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:12.241][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:12.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.243][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:12.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:12.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.255][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:12.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:12.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.259][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:12.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:12.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.263][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:12.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:12.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.267][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:12.268][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:12.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.270][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.271][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:12.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:12.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:03:12.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:03:12.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:03:12.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:03:12.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:03:12.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:03:12.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.294][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:03:12.295][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:03:12.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.297][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:03:12.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:03:12.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.309][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:12.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:12.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.313][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:12.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:12.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.318][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:12.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:12.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.322][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:12.323][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:12.324][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.325][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.326][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:12.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:12.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.337][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:12.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:12.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.341][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:12.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:12.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.345][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:12.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:12.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.349][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:12.350][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:12.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.352][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.358][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:12.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:12.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.369][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:12.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:12.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.373][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:12.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:12.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.377][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:12.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:12.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.381][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:12.383][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:12.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.385][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.386][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:12.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:12.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.397][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:12.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:12.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.401][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:12.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:12.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.405][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:12.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:12.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.410][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:12.411][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:12.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.413][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.414][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:12.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:12.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.424][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:03:12.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:03:12.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.428][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:03:12.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:03:12.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.433][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:03:12.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:03:12.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.437][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:03:12.438][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:03:12.439][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.440][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.441][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:03:12.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:03:12.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:12.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:12.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:12.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:12.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:12.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:12.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.464][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:12.465][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:12.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.467][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:12.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:12.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.479][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:12.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:12.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.483][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:12.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:12.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.487][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:12.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:12.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.491][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:12.492][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:12.493][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.494][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.495][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:12.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:12.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.512][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:12.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:12.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.516][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:12.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:12.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.520][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:12.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:12.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.524][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:12.525][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:12.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.527][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.528][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:12.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:12.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.539][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:12.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:12.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.543][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:12.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:12.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.547][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:12.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:12.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.552][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:12.553][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:12.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.555][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.556][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:12.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:12.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.566][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:03:12.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:03:12.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.571][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:03:12.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:03:12.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.575][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:03:12.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:03:12.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.579][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:03:12.580][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:03:12.581][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.582][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.583][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:03:12.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:03:12.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.594][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:12.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:12.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:12.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:12.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.602][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:12.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:12.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.606][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:12.607][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:12.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.609][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.610][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:12.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:12.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.621][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:12.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:12.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.625][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:12.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:12.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.629][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:12.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:12.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.633][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:12.634][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:12.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.636][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.637][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:12.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:12.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.648][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:12.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:12.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.657][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:12.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:12.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.661][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:12.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:12.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.665][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:12.667][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:12.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.669][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.670][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:12.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:12.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.680][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.682][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.683][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.688][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:03:12.689][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:03:12.690][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.691][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.695][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:12.696][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:12.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.698][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.702][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:03:12.703][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:03:12.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.705][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.709][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:12.710][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:12.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.712][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.716][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:12.717][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:12.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.719][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.723][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:12.724][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:12.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.726][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.730][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:12.732][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:12.733][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.734][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.738][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:12.739][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:12.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.741][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.745][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:12.746][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:12.747][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.748][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.752][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:12.753][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:12.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.755][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.759][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:12.760][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:12.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.762][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.766][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:12.767][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:12.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.769][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.773][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:12.774][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:12.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.776][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.780][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:12.782][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:12.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.784][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.788][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:12.789][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:12.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.791][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.795][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:12.801][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:12.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.803][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.807][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:03:12.808][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:03:12.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.810][ef$get] fields variable is a list.
biodb.INFO [2025-09-20 16:03:12.817][biodb::testThat]
biodb.INFO [2025-09-20 16:03:12.818][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-09-20 16:03:12.819][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:03:12.820][biodb::testThat]
biodb.DEBUG[2025-09-20 16:03:12.834][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-09-20 16:03:12.841][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-20 16:03:12.846][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-20 16:03:12.848][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-09-20 16:03:12.850][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-09-20 16:03:12.851][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-20 16:03:12.853][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-09-20 16:03:12.855][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-09-20 16:03:12.879][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-09-20 16:03:12.880][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-09-20 16:03:12.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-20 16:03:12.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:12.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:12.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:12.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:12.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:12.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-20 16:03:12.895][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.896][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.898][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:12.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:12.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.904][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:12.905][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:12.906][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.907][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.908][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:12.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:12.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.912][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:03:12.913][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:03:12.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.915][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.917][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:03:12.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:03:12.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.921][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:12.922][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:12.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.924][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.925][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:12.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:12.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.929][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:03:12.931][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:03:12.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.932][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:03:12.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:03:12.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.938][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:12.939][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:12.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.941][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:12.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:12.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.953][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:12.954][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:12.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.956][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.957][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:12.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:12.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.961][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:12.962][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:12.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.964][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.965][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:12.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:12.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.969][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:12.971][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:12.972][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.973][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.974][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:12.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:12.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.978][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:12.979][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:12.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.981][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.982][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:12.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:12.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.987][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:12.988][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:12.989][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.990][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.991][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:12.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:12.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:12.995][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:12.996][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:12.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:12.998][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.000][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:13.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:13.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.004][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:13.005][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:13.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.007][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.008][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:13.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:13.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.012][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:13.013][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:13.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.015][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:13.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:13.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.021][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.022][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.024][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.025][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.029][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:13.030][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:13.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.032][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.034][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:13.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:13.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.038][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:03:13.039][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:03:13.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.041][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.042][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:03:13.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:03:13.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.046][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-09-20 16:03:13.047][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:13.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.049][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.051][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-09-20 16:03:13.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:13.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:13.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:13.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:13.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:13.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:13.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:13.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.067][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:03:13.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:03:13.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.072][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:03:13.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:03:13.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.076][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:03:13.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:03:13.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.080][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:13.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:13.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.084][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:13.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:13.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.088][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:13.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:13.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:03:13.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:03:13.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.101][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:03:13.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:03:13.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:03:13.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:03:13.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:13.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:13.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:13.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:13.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:13.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:03:13.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.122][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:13.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:13.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.126][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:13.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:13.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.130][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:13.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:03:13.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.134][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:13.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:13.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.138][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:13.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:13.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.142][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:13.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:03:13.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.147][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:13.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:13.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.151][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:13.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:13.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.155][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:13.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:03:13.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.159][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:13.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:13.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.163][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:13.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:13.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.167][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:13.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:13.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.171][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:13.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:13.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.175][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:13.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:13.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.179][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:13.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:13.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.184][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:13.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:13.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:13.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:13.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.192][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:13.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:13.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.196][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:13.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:13.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.200][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:13.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:13.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.204][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:13.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:13.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.208][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:13.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:13.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.213][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:13.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:13.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.217][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:13.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:03:13.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.221][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:13.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:13.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:13.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:13.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:13.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:03:13.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.233][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.237][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.241][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.250][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:13.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:13.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.254][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:13.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:13.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.258][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:13.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:03:13.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.263][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.267][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.271][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.275][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:03:13.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:03:13.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.279][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:03:13.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:03:13.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.283][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:03:13.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:03:13.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.287][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-09-20 16:03:13.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:13.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.292][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:13.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:13.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.296][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:13.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:13.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.300][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:13.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:13.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.304][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-09-20 16:03:13.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:13.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.309][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.313][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.317][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.321][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.325][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.330][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:13.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:13.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.334][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:13.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:13.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:13.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:13.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.342][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:13.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:03:13.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:13.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:13.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:13.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:13.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:13.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:13.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:13.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:13.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:13.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:13.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:13.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:13.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-20 16:03:13.371][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-09-20 16:03:13.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-09-20 16:03:13.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-09-20 16:03:13.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-09-20 16:03:13.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-09-20 16:03:13.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-09-20 16:03:13.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-09-20 16:03:13.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-09-20 16:03:13.396][biodb::testThat]
biodb.INFO [2025-09-20 16:03:13.397][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-09-20 16:03:13.398][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:03:13.399][biodb::testThat]
biodb.TRACE[2025-09-20 16:03:13.402][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.403][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.405][ef$get] fields variable is a list.
biodb.DEBUG[2025-09-20 16:03:13.406][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2025-09-20 16:03:13.431][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.435][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.439][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-20 16:03:13.446][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2025-09-20 16:03:13.447][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-09-20 16:03:13.448][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-09-20 16:03:13.449][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-09-20 16:03:13.451][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-20 16:03:13.452][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-20 16:03:13.454][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-09-20 16:03:13.455][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-20 16:03:13.456][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-09-20 16:03:13.458][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-09-20 16:03:13.459][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-09-20 16:03:13.460][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-09-20 16:03:13.461][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-09-20 16:03:13.462][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-09-20 16:03:13.463][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-09-20 16:03:13.465][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-20 16:03:13.481][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-09-20 16:03:13.482][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-09-20 16:03:13.483][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-09-20 16:03:13.493][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:13.494][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:13.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.496][ef$get] fields variable is a list.
biodb.DEBUG[2025-09-20 16:03:13.498][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2025-09-20 16:03:13.508][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:13.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:13.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.512][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:13.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:13.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.516][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:13.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:13.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-20 16:03:13.522][function(conn, opt)] With value "1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.".
biodb.DEBUG[2025-09-20 16:03:13.581][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-09-20 16:03:13.582][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-09-20 16:03:13.584][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-09-20 16:03:13.598][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-20 16:03:13.599][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-20 16:03:13.601][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-09-20 16:03:13.602][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-20 16:03:13.603][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-09-20 16:03:13.618][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-09-20 16:03:13.619][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-09-20 16:03:13.620][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-09-20 16:03:13.621][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-09-20 16:03:13.623][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-09-20 16:03:13.623][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-09-20 16:03:13.625][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:13.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:13.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.630][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:13.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:13.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.634][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:13.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:13.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.638][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:13.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:13.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-20 16:03:13.642][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-09-20 16:03:13.643][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-09-20 16:03:13.644][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-09-20 16:03:13.660][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.661][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.662][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.663][ef$get] fields variable is a list.
biodb.DEBUG[2025-09-20 16:03:13.664][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2025-09-20 16:03:13.674][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.679][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.683][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-20 16:03:13.689][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2025-09-20 16:03:13.691][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2025-09-20 16:03:13.692][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-09-20 16:03:13.693][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-09-20 16:03:13.694][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-20 16:03:13.696][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-20 16:03:13.697][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-09-20 16:03:13.699][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-20 16:03:13.699][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-09-20 16:03:13.701][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-09-20 16:03:13.702][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-09-20 16:03:13.703][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-09-20 16:03:13.704][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-09-20 16:03:13.705][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-09-20 16:03:13.706][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-09-20 16:03:13.708][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.712][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.716][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.720][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:13.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-20 16:03:13.724][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-09-20 16:03:13.725][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-09-20 16:03:13.726][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2025-09-20 16:03:13.739][biodb::testThat]
biodb.INFO [2025-09-20 16:03:13.740][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-09-20 16:03:13.741][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:03:13.742][biodb::testThat]
biodb.TRACE[2025-09-20 16:03:13.752][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.756][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.760][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-20 16:03:13.774][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-09-20 16:03:13.775][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-09-20 16:03:13.776][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-09-20 16:03:13.777][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-20 16:03:13.779][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-20 16:03:13.780][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-09-20 16:03:13.781][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-20 16:03:13.782][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-09-20 16:03:13.784][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-09-20 16:03:13.785][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-09-20 16:03:13.786][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-09-20 16:03:13.787][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-09-20 16:03:13.788][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-09-20 16:03:13.789][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-09-20 16:03:13.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.808][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:13.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:13.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-20 16:03:13.812][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-09-20 16:03:13.813][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2025-09-20 16:03:13.826][biodb::testThat]
biodb.INFO [2025-09-20 16:03:13.827][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-09-20 16:03:13.828][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:03:13.829][biodb::testThat]
biodb.TRACE[2025-09-20 16:03:13.849][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-20 16:03:13.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-20 16:03:13.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.853][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-20 16:03:13.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-20 16:03:13.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.857][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-20 16:03:13.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-20 16:03:13.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.861][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-20 16:03:13.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-20 16:03:13.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.905][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-20 16:03:13.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-20 16:03:13.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.909][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-20 16:03:13.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-20 16:03:13.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.914][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-20 16:03:13.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-20 16:03:13.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:13.918][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-20 16:03:13.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-20 16:03:13.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:13.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-09-20 16:03:13.931][biodb::testThat]
biodb.INFO [2025-09-20 16:03:13.932][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-09-20 16:03:13.933][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:03:13.934][biodb::testThat]
biodb.INFO [2025-09-20 16:03:13.941][biodb::testThat]
biodb.INFO [2025-09-20 16:03:13.942][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-09-20 16:03:13.943][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:03:13.944][biodb::testThat]
biodb.INFO [2025-09-20 16:03:13.951][biodb::testThat]
biodb.INFO [2025-09-20 16:03:13.952][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-09-20 16:03:13.953][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:03:13.954][biodb::testThat]
biodb.DEBUG[2025-09-20 16:03:13.957][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-09-20 16:03:14.875][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-09-20 16:03:14.945][biodb::testThat]
biodb.INFO [2025-09-20 16:03:14.947][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-09-20 16:03:14.950][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:03:14.952][biodb::testThat]
biodb.DEBUG[2025-09-20 16:03:15.050][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-09-20 16:03:15.086][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:15.088][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:15.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:15.091][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:15.093][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:15.094][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:15.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:15.097][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:15.099][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:15.100][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:15.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:15.103][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:15.105][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:15.107][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:15.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:15.109][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:15.111][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:03:15.112][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:03:15.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:15.115][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:15.116][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:15.118][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:03:15.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:15.120][ef$get] fields variable is a list.
biodb.INFO [2025-09-20 16:03:15.122][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-09-20 16:03:15.123][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-09-20 16:03:15.124][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-09-20 16:03:15.126][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-20 16:03:15.127][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:15.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:15.129][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:15.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:15.131][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:15.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 147 ]
> 
> proc.time()
   user  system elapsed 
  5.246   0.300   6.398

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

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

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.14.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor ‘EntryMaker::EntryMaker()’:
EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)