Back to Long Tests report for BioC 3.21

This page was generated on 2025-09-06 23:55 -0400 (Sat, 06 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
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: 2025-09-06 09:55 -0400 (Sat, 06 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  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on merida1

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

raw results


Summary

Package: biodbHmdb
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.14.0.tar.gz
StartedAt: 2025-09-06 16:01:16 -0400 (Sat, 06 Sep 2025)
EndedAt: 2025-09-06 16:02:41 -0400 (Sat, 06 Sep 2025)
EllapsedTime: 85.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-09-06 16:02:35.350][biodb::testContext]
biodb.INFO [2025-09-06 16:02:35.354][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-06 16:02:35.356][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-09-06 16:02:35.357][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-06 16:02:35.358][biodb::testContext]
biodb.INFO [2025-09-06 16:02:35.365][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-09-06 16:02:35.367][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-09-06 16:02:35.374][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:02:35.376][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-06 16:02:35.377][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-06 16:02:35.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:35.382][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-06 16:02:35.407][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-06 16:02:35.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.410][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:35.411][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-06 16:02:35.413][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-06 16:02:35.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:35.417][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-06 16:02:35.419][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-06 16:02:35.420][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-06 16:02:35.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.423][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:35.425][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-06 16:02:35.426][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-06 16:02:35.427][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-06 16:02:35.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:35.432][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-06 16:02:35.433][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-06 16:02:35.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.437][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:35.438][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-06 16:02:35.439][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-06 16:02:35.440][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-06 16:02:35.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:35.445][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-06 16:02:35.446][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-06 16:02:35.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.450][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:35.451][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-06 16:02:35.452][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-06 16:02:35.453][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-06 16:02:35.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:35.458][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-06 16:02:35.459][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-06 16:02:35.461][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-06 16:02:35.462][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-06 16:02:35.463][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-06 16:02:35.465][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-06 16:02:35.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.468][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:35.469][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-06 16:02:35.471][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-06 16:02:35.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:35.475][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-06 16:02:35.477][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-06 16:02:35.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.480][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:35.481][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-06 16:02:35.482][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-06 16:02:35.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:35.487][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-06 16:02:35.488][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-09-06 16:02:35.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.492][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:35.493][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-06 16:02:35.494][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-06 16:02:35.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:35.499][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-06 16:02:35.500][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-06 16:02:35.510][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-06 16:02:35.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.514][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:35.515][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-06 16:02:35.517][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-06 16:02:35.518][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-06 16:02:35.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:35.525][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-06 16:02:35.575][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:35.596][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-09-06 16:02:35.598][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:35.599][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:02:35.600][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:35.601][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:02:35.603][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:35.604][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:02:35.605][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-06 16:02:35.606][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:02:35.608][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:35.609][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-06 16:02:35.610][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:02:35.611][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:35.613][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:35.614][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:02:35.614][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:02:35.614][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:02:35.614][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-06 16:02:35.614][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-06 16:02:35.615][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:02:35.616][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:35.617][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:35.619][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:02:35.620][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:35.621][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:35.622][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:02:35.623][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:35.625][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:02:35.626][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:02:35.627][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:35.628][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:35.630][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-06 16:02:35.632][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:35.633][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-06 16:02:35.634][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:35.635][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:02:35.637][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:35.638][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:02:35.639][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:35.641][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:02:35.642][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-06 16:02:35.643][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:02:35.645][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:35.646][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-06 16:02:35.647][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:02:35.648][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:35.650][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:35.651][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:02:35.651][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:02:35.651][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:02:35.651][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-06 16:02:35.651][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-06 16:02:35.652][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:02:35.654][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:35.655][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:35.656][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:02:35.657][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:35.658][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:35.659][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:02:35.661][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:35.662][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:02:35.663][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:02:35.664][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:35.666][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:35.667][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-06 16:02:35.669][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:35.671][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-09-06 16:02:35.672][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:35.673][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:02:35.674][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:35.676][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:02:35.677][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:35.678][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:02:35.679][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-06 16:02:35.681][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:02:35.682][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:35.683][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-06 16:02:35.685][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:02:35.686][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:35.687][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:35.688][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:35.690][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:02:35.691][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:35.692][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:35.693][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:02:35.694][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:35.696][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:35.697][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:02:35.698][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:35.699][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:02:35.700][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:02:35.702][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:35.704][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:35.705][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-06 16:02:35.707][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:35.709][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-06 16:02:35.710][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:35.711][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:02:35.713][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:35.714][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:02:35.715][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:35.716][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:02:35.718][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-06 16:02:35.719][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:02:35.720][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:35.721][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-06 16:02:35.723][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:02:35.724][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:35.725][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:35.726][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:35.728][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:02:35.729][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:35.730][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:35.731][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:02:35.733][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:35.734][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:35.735][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:02:35.736][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:35.737][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:02:35.739][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:02:35.740][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:35.741][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:35.745][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:02:35.746][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.748][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:35.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:35.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:35.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:35.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:35.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:35.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:35.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:35.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:35.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:35.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:35.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:35.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.770][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:35.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:35.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:35.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:35.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:35.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:35.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.782][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:35.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:35.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:35.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.788][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:35.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:35.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:35.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.793][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:35.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:35.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:35.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:35.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:35.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:35.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:35.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:35.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:35.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.814][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:35.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:35.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:35.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.820][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:35.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:35.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:35.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.825][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:35.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:35.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:35.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.831][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:35.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:35.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:35.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:35.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:35.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:35.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.842][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:35.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:35.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:35.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:35.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:35.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:35.849][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-06 16:02:35.854][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-06 16:02:35.855][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-06 16:02:35.857][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-06 16:02:35.859][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-06 16:02:35.860][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-06 16:02:35.862][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-06 16:02:35.864][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-06 16:02:35.866][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-06 16:02:35.867][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-06 16:02:35.869][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-06 16:02:35.871][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-06 16:02:35.872][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-06 16:02:35.874][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-06 16:02:35.876][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-06 16:02:35.877][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-06 16:02:35.879][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-06 16:02:35.881][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-06 16:02:35.883][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-06 16:02:35.884][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-06 16:02:35.886][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-06 16:02:35.888][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-06 16:02:35.890][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-06 16:02:35.891][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-06 16:02:35.893][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-06 16:02:35.895][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-06 16:02:35.896][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-06 16:02:35.898][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-06 16:02:35.900][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-06 16:02:35.901][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-06 16:02:35.903][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-06 16:02:35.905][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-06 16:02:35.906][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-06 16:02:35.908][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-06 16:02:35.910][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-06 16:02:35.911][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-06 16:02:35.913][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-06 16:02:35.915][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-06 16:02:35.916][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-06 16:02:35.918][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-06 16:02:35.920][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-06 16:02:35.922][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-06 16:02:35.923][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-06 16:02:35.925][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-06 16:02:35.927][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-06 16:02:35.928][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-06 16:02:35.930][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-06 16:02:35.932][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-06 16:02:35.933][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-06 16:02:35.935][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-06 16:02:35.937][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-06 16:02:35.938][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-06 16:02:35.940][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-06 16:02:35.942][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-06 16:02:35.943][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-06 16:02:35.945][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-06 16:02:35.947][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-06 16:02:35.949][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-06 16:02:35.950][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-06 16:02:35.952][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-06 16:02:35.954][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-06 16:02:35.955][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-06 16:02:35.957][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-06 16:02:35.959][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-06 16:02:35.961][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-06 16:02:35.962][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-06 16:02:35.964][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-06 16:02:35.966][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-06 16:02:35.968][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-06 16:02:35.969][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-06 16:02:35.971][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-06 16:02:35.973][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-06 16:02:35.975][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-06 16:02:35.976][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-06 16:02:35.978][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-06 16:02:35.980][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-06 16:02:35.981][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-06 16:02:35.983][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-06 16:02:35.985][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-06 16:02:35.987][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-06 16:02:35.988][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-06 16:02:35.990][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-06 16:02:35.992][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-06 16:02:35.999][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-06 16:02:36.001][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-09-06 16:02:36.005][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:02:36.006][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.008][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.009][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[2025-09-06 16:02:36.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:36.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.027][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[2025-09-06 16:02:36.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:36.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.035][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:36.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:36.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.043][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:36.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:36.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.050][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:36.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:36.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.058][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:36.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:36.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.066][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:36.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:36.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.073][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:36.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:36.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.081][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:36.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:36.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.089][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:36.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:36.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.097][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:36.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:36.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.105][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:36.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:36.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.113][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:36.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:36.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:36.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:36.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.129][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:36.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:36.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.137][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:36.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:36.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:36.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:36.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.153][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:36.154][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-09-06 16:02:36.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:36.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:36.164][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-09-06 16:02:36.177][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-09-06 16:02:36.179][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:36.181][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-09-06 16:02:36.182][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:36.183][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:02:36.184][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:36.186][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-09-06 16:02:36.187][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:36.188][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:02:36.189][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-06 16:02:36.191][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:02:36.192][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:36.193][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-09-06 16:02:36.194][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:02:36.196][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-09-06 16:02:36.196][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-09-06 16:02:36.196][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-09-06 16:02:36.196][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-09-06 16:02:36.196][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-09-06 16:02:36.196][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-09-06 16:02:36.196][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-09-06 16:02:36.196][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-09-06 16:02:36.196][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-09-06 16:02:36.196][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-09-06 16:02:36.196][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-09-06 16:02:36.196][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-09-06 16:02:36.196][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-09-06 16:02:36.196][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-09-06 16:02:36.196][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-09-06 16:02:36.196][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-09-06 16:02:36.196][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-09-06 16:02:36.196][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-09-06 16:02:36.197][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:36.199][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:02:36.199][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-09-06 16:02:36.199][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-09-06 16:02:36.200][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-06 16:02:36.201][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:36.202][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:36.204][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:02:36.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:36.206][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:36.207][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:02:36.208][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-09-06 16:02:36.208][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-09-06 16:02:36.210][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:02:36.211][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:02:36.212][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:36.213][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:36.221][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-09-06 16:02:36.223][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-06 16:02:36.225][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-06 16:02:36.227][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-06 16:02:36.228][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-06 16:02:36.272][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-09-06 16:02:36.273][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-09-06 16:02:36.278][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-09-06 16:02:36.282][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-09-06 16:02:36.286][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-06 16:02:36.287][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-06 16:02:36.288][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-09-06 16:02:36.290][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-09-06 16:02:36.299][biodb::testThat]
biodb.INFO [2025-09-06 16:02:36.301][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-09-06 16:02:36.302][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:02:36.303][biodb::testThat]
biodb.TRACE[2025-09-06 16:02:36.307][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-09-06 16:02:36.309][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-09-06 16:02:36.313][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-09-06 16:02:36.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-06 16:02:36.322][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:36.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:36.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:36.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:36.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:36.343][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:02:36.354][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:36.356][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:36.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.358][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:36.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:36.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.382][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:36.383][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:36.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.385][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.422][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:36.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:36.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.427][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:36.429][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:36.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.431][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.433][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:36.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:36.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.438][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:36.439][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:36.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.442][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.443][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:36.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:36.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.449][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:36.450][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:36.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.453][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:36.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:36.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.460][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:36.461][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:36.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.463][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:36.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:36.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.470][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:36.472][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:36.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.474][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.476][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:36.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:36.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.481][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:36.483][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:36.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.485][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.487][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:36.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:36.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.500][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:36.502][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:36.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.504][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.506][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:36.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:36.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.511][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:36.512][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:36.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.514][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.516][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:36.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:36.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.521][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:36.522][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:36.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.525][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.526][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:36.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:36.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.531][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:36.533][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:36.534][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.535][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:36.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:36.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.542][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:36.543][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:36.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.546][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.547][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:36.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:36.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.553][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:36.554][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:36.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.556][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:36.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:36.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.563][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:36.565][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:36.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.567][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.569][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:36.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:36.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.574][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:36.575][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:36.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.578][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.579][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:36.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:36.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.585][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:36.586][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:36.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.588][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.590][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:36.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:36.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.595][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-09-06 16:02:36.597][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:36.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.599][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.601][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-09-06 16:02:36.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:36.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:36.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:36.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:36.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:36.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:36.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:36.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.665][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:36.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:36.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.670][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:36.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:36.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.678][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:36.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:36.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.683][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:36.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:36.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.688][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:36.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:36.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.693][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:36.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:36.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:36.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:36.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:36.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:36.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:36.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:36.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:36.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:36.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:36.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:36.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:36.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:36.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.728][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:36.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:36.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.733][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:36.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:36.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.738][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:36.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:36.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.743][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:36.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:36.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.748][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:36.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:36.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.753][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:36.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:36.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.758][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:36.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:36.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.763][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:36.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:36.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.768][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:36.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:36.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.773][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:36.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:36.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.778][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:36.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:36.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.783][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:36.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:36.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.788][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:36.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:36.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.793][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:36.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:36.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.798][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:36.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:36.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.803][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:36.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:36.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.808][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:36.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:36.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.813][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:36.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:36.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.818][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:36.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:36.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.823][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:36.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:36.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.828][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:36.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:36.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.834][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:36.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:36.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.839][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:36.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:36.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.844][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:36.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:36.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:36.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:36.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:36.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:36.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:36.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:36.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.867][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:36.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:36.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.872][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:36.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:36.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.877][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:36.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:36.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.882][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:36.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:36.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.886][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:36.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:36.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.891][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:36.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:36.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.896][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:36.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:36.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.901][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:36.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:36.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.906][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:36.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:36.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.911][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:36.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:36.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.916][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:36.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:36.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.921][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:36.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:36.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.925][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-09-06 16:02:36.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:36.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.930][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:36.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:36.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.935][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:36.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:36.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.940][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:36.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:36.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.945][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-09-06 16:02:36.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:36.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.973][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:36.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:36.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.978][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:36.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:36.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.983][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:36.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:36.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.988][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:36.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:36.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.993][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:36.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:36.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:36.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:36.998][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:36.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:37.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.003][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:37.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:37.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.013][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:37.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:37.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:02:37.052][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-09-06 16:02:37.055][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:02:37.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:02:37.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.060][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:02:37.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:02:37.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.065][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-06 16:02:37.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-06 16:02:37.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.070][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-06 16:02:37.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-06 16:02:37.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.113][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:37.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:37.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.156][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:37.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:37.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.161][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:37.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:37.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.166][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:37.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:37.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.194][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.196][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.197][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.198][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.214][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:37.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:37.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.220][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:37.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:37.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.225][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:37.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:37.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.234][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:37.236][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:37.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.238][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.239][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:37.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:37.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:37.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:37.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:37.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:37.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:37.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:37.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.269][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:37.270][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:37.271][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.272][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:37.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:37.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.288][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:37.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:37.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.293][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:37.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:37.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.298][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:37.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:37.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.304][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:37.306][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:37.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.308][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.309][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:37.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:37.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:37.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:37.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:37.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:37.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:37.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:37.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.340][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:37.341][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:37.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.343][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:37.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:37.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.360][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:37.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:37.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.365][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:37.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:37.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.370][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:37.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:37.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.375][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:37.377][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:37.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.379][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.380][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:37.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:37.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:37.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:37.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.400][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:37.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:37.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.405][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:37.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:37.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.410][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:37.412][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:37.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.414][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.416][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:37.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:37.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.435][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:37.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:37.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.440][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:37.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:37.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.445][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:37.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:37.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.450][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:37.451][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:37.452][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.454][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.455][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:37.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:37.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.470][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:37.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:37.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.475][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:37.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:37.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.480][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:37.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:37.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.485][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:37.486][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:37.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.489][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.490][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:37.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:37.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.505][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:37.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:37.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.510][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:37.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:37.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.515][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:37.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:37.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.520][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:37.522][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:37.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.524][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.525][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:37.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:37.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:37.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:37.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:37.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:37.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:37.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:37.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.564][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:37.565][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:37.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.567][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:37.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:37.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.591][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:37.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:37.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.597][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:37.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:37.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.602][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:37.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:37.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.607][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:37.608][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:37.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.610][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.612][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:37.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:37.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.632][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:37.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:37.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.637][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:37.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:37.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.642][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:37.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:37.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.647][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:37.648][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:37.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.650][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.651][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:37.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:37.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.666][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:37.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:37.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.671][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:37.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:37.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.676][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:37.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:37.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.681][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:37.683][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:37.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.685][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.686][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:37.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:37.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.701][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:37.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:37.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.706][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:37.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:37.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.711][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:37.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:37.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.716][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:37.717][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:37.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.720][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.721][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:37.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:37.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.736][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:37.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:37.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.741][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:37.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:37.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:37.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:37.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.752][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:37.753][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:37.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.756][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:37.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:37.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.772][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:37.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:37.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:37.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:37.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.782][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:37.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:37.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.787][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:37.789][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:37.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.791][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.792][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:37.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:37.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.807][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:37.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:37.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.812][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:37.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:37.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.821][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:37.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:37.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.826][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:37.828][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:37.829][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.830][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.831][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:37.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:37.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.846][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:37.848][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:37.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.850][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.856][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:37.857][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:37.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.860][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.866][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:37.868][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:37.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.870][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.876][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:37.878][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:37.879][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.880][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.886][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:37.888][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:37.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.890][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.896][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:37.898][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:37.899][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.900][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.906][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:37.908][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:37.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.910][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.916][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:37.918][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:37.919][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.920][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.926][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:37.928][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:37.929][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.930][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.936][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:37.938][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:37.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.940][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.947][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:37.948][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:37.949][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.950][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.957][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:37.958][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:37.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.961][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.967][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:37.969][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:37.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.971][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.977][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:37.979][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:37.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.981][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.987][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:37.989][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:37.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:37.991][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:37.997][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:37.999][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:38.000][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.001][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.008][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:38.009][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:38.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.012][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.023][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:38.024][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:38.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.027][ef$get] fields variable is a list.
biodb.INFO [2025-09-06 16:02:38.037][biodb::testThat]
biodb.INFO [2025-09-06 16:02:38.038][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-09-06 16:02:38.039][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:02:38.041][biodb::testThat]
biodb.DEBUG[2025-09-06 16:02:38.059][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-09-06 16:02:38.066][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-06 16:02:38.071][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-06 16:02:38.073][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-09-06 16:02:38.076][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-09-06 16:02:38.077][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-06 16:02:38.124][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-09-06 16:02:38.125][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-09-06 16:02:38.157][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-09-06 16:02:38.159][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-09-06 16:02:38.161][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-06 16:02:38.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:38.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:38.170][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:38.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:38.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:38.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-06 16:02:38.177][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:38.179][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:38.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.181][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:38.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:38.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.188][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:38.189][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:38.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.192][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.193][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:38.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:38.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.199][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:38.200][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:38.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.202][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.204][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:38.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:38.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.209][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:38.210][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:38.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.213][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.215][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:38.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:38.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.220][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:38.221][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:38.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.223][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:38.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:38.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.230][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:38.232][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:38.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.234][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:38.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:38.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.241][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:38.242][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:38.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.249][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.251][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:38.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:38.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.256][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:38.257][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:38.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.260][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.261][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:38.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:38.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.266][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:38.268][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:38.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.270][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.272][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:38.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:38.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.277][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:38.278][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:38.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.280][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.282][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:38.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:38.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.287][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:38.288][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:38.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.291][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.293][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:38.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:38.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.298][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:38.299][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:38.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.302][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.303][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:38.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:38.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.308][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:38.310][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:38.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.312][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.314][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:38.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:38.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.319][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:38.320][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:38.322][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.323][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.324][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:38.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:38.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.330][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:38.331][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:38.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.333][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:38.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:38.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.340][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:38.341][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:38.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.344][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.345][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:38.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:38.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.350][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:38.352][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:38.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.354][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.356][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:38.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:38.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.361][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-09-06 16:02:38.362][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:38.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.365][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.366][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-09-06 16:02:38.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:38.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:38.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:38.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:38.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:38.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:38.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:38.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.387][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:38.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:38.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.392][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:38.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:38.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.397][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:38.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:38.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.402][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:38.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:38.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.407][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:38.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:38.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.412][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:38.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:38.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:38.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:38.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:38.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:38.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:38.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:38.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:38.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:38.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:38.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:38.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:38.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:38.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.452][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:38.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:38.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.457][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:38.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:38.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.462][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:38.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:38.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.467][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:38.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:38.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.472][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:38.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:38.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.477][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:38.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:38.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.482][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:38.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:38.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.487][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:38.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:38.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.492][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:38.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:38.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.497][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:38.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:38.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.502][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:38.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:38.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.507][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:38.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:38.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.512][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:38.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:38.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.517][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:38.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:38.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.522][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:38.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:38.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.527][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:38.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:38.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.532][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:38.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:38.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:38.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:38.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.542][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:38.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:38.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.547][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:38.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:38.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.552][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:38.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:38.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.557][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:38.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:38.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.563][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:38.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:38.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.568][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:38.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:38.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:38.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:38.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:38.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:38.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:38.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:38.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.588][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:38.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:38.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.593][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:38.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:38.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:38.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:38.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.603][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:38.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:38.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.612][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:38.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:38.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.618][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:38.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:38.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.623][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:38.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:38.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.628][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:38.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:38.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.633][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:38.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:38.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.638][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:38.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:38.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.643][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:38.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:38.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.648][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:38.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:38.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.653][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-09-06 16:02:38.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:38.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.659][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:38.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:38.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.664][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:38.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:38.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.669][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:38.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:38.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.674][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-09-06 16:02:38.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:38.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.680][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:38.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:38.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.685][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:38.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:38.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.690][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:38.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:38.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:38.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:38.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:38.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:38.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.706][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:38.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:38.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.711][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:38.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:38.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:38.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:38.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.722][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:38.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:38.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:38.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:38.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:38.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:38.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:38.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:38.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:38.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:38.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:38.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:38.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:38.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:38.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:02:38.758][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-09-06 16:02:38.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-09-06 16:02:38.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-09-06 16:02:38.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-09-06 16:02:38.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-09-06 16:02:38.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-09-06 16:02:38.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-09-06 16:02:38.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-09-06 16:02:38.784][biodb::testThat]
biodb.INFO [2025-09-06 16:02:38.785][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-09-06 16:02:38.786][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:02:38.791][biodb::testThat]
biodb.TRACE[2025-09-06 16:02:38.794][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:38.796][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:38.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.798][ef$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:02:38.800][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2025-09-06 16:02:38.833][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:38.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:38.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.838][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:38.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:38.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.843][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:38.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:38.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:02:38.852][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2025-09-06 16:02:38.853][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-09-06 16:02:38.854][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-09-06 16:02:38.856][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-09-06 16:02:38.858][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-06 16:02:38.859][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-06 16:02:38.861][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-09-06 16:02:38.863][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-06 16:02:38.864][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-09-06 16:02:38.866][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-09-06 16:02:38.867][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-09-06 16:02:38.868][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-09-06 16:02:38.869][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-09-06 16:02:38.871][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-09-06 16:02:38.872][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-09-06 16:02:38.874][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:38.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:38.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.879][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:38.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:38.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.884][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:38.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:38.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.889][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:38.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:38.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:02:38.894][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-09-06 16:02:38.895][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-09-06 16:02:38.896][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-09-06 16:02:38.911][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:38.913][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:38.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.915][ef$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:02:38.917][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2025-09-06 16:02:38.933][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:38.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:38.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.938][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:38.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:38.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:38.943][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:38.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:38.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:38.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:02:38.951][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[2025-09-06 16:02:39.025][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-09-06 16:02:39.027][private$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[2025-09-06 16:02:39.028][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-09-06 16:02:39.047][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-06 16:02:39.048][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-06 16:02:39.050][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-09-06 16:02:39.052][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-06 16:02:39.053][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-09-06 16:02:39.073][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-09-06 16:02:39.075][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-09-06 16:02:39.076][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-09-06 16:02:39.077][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-09-06 16:02:39.078][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-09-06 16:02:39.080][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-09-06 16:02:39.082][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:39.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:39.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.087][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:39.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:39.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.092][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:39.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:39.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.097][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:39.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:39.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:02:39.102][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-09-06 16:02:39.103][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-09-06 16:02:39.104][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-09-06 16:02:39.119][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:39.121][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:39.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.127][ef$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:02:39.128][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2025-09-06 16:02:39.143][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:39.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:39.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.149][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:39.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:39.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.153][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:39.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:39.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:02:39.161][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2025-09-06 16:02:39.163][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2025-09-06 16:02:39.164][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-09-06 16:02:39.166][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-09-06 16:02:39.168][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-06 16:02:39.170][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-06 16:02:39.171][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-09-06 16:02:39.173][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-06 16:02:39.174][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-09-06 16:02:39.176][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-09-06 16:02:39.177][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-09-06 16:02:39.178][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-09-06 16:02:39.180][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-09-06 16:02:39.181][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-09-06 16:02:39.182][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-09-06 16:02:39.184][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:39.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:39.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.189][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:39.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:39.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.194][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:39.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:39.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.200][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:39.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:39.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:02:39.205][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-09-06 16:02:39.206][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-09-06 16:02:39.207][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2025-09-06 16:02:39.226][biodb::testThat]
biodb.INFO [2025-09-06 16:02:39.228][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-09-06 16:02:39.229][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:02:39.230][biodb::testThat]
biodb.TRACE[2025-09-06 16:02:39.244][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:39.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:39.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.249][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:39.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:39.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.254][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:39.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:39.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:02:39.272][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-09-06 16:02:39.273][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-09-06 16:02:39.274][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-09-06 16:02:39.276][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-06 16:02:39.278][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-06 16:02:39.280][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-09-06 16:02:39.281][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-06 16:02:39.283][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-09-06 16:02:39.284][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-09-06 16:02:39.286][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-09-06 16:02:39.287][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-09-06 16:02:39.288][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-09-06 16:02:39.289][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-09-06 16:02:39.291][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-09-06 16:02:39.293][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:39.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:39.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.298][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:39.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:39.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.303][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:39.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:39.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.308][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:39.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:39.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:02:39.317][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-09-06 16:02:39.319][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2025-09-06 16:02:39.338][biodb::testThat]
biodb.INFO [2025-09-06 16:02:39.339][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-09-06 16:02:39.340][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:02:39.342][biodb::testThat]
biodb.TRACE[2025-09-06 16:02:39.368][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:02:39.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:02:39.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.373][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:02:39.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:02:39.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.378][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-06 16:02:39.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-06 16:02:39.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.383][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-06 16:02:39.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-06 16:02:39.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.445][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:02:39.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:02:39.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.450][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:02:39.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:02:39.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.455][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-06 16:02:39.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-06 16:02:39.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:39.460][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-06 16:02:39.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-06 16:02:39.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:39.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-09-06 16:02:39.473][biodb::testThat]
biodb.INFO [2025-09-06 16:02:39.474][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-09-06 16:02:39.475][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:02:39.476][biodb::testThat]
biodb.INFO [2025-09-06 16:02:39.490][biodb::testThat]
biodb.INFO [2025-09-06 16:02:39.491][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-09-06 16:02:39.493][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:02:39.494][biodb::testThat]
biodb.INFO [2025-09-06 16:02:39.504][biodb::testThat]
biodb.INFO [2025-09-06 16:02:39.505][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-09-06 16:02:39.506][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:02:39.507][biodb::testThat]
biodb.DEBUG[2025-09-06 16:02:39.512][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-09-06 16:02:39.805][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-09-06 16:02:40.211][biodb::testThat]
biodb.INFO [2025-09-06 16:02:40.212][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-09-06 16:02:40.214][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:02:40.215][biodb::testThat]
biodb.DEBUG[2025-09-06 16:02:40.384][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-09-06 16:02:40.565][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:40.566][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:40.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:40.569][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:40.570][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:40.571][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:40.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:40.574][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:40.575][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:40.576][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:40.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:40.578][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:40.580][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:40.581][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:40.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:40.583][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:40.585][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:40.586][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:40.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:40.588][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:40.590][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:40.591][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:40.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:40.594][ef$get] fields variable is a list.
biodb.INFO [2025-09-06 16:02:40.595][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-09-06 16:02:40.633][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-09-06 16:02:40.635][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-09-06 16:02:40.637][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-06 16:02:40.638][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:40.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:40.640][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:40.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:40.642][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:40.643][FUN] Functions in observer 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 3 | WARN 0 | SKIP 0 | PASS 144 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_long_100_generic.R:42:1'): The entry page URL can be downloaded. ──
!is.na(content) is not TRUE

`actual`:       
`expected`: TRUE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.na(content))
── Failure ('test_long_100_generic.R:42:1'): The entry page URL can be downloaded. ──
nchar(content) > 0 is not TRUE

`actual`:       
`expected`: TRUE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(nchar(content) > 0)
── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
Error in `charToRaw(content)`: argument must be a character vector of length 1
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─biodb:::getUrlContent(url, binary = TRUE)
 4.     └─biodb:::getBaseUrlContent(u, binary = binary)
 5.       └─base::charToRaw(content)

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 144 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.14.0’
* 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 ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─testthat::expect_true(nchar(content) > 0)
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 144 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/Users/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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c EntryMaker.cpp -o EntryMaker.o
EntryMaker.cpp:6:5: warning: field 'accession_tag' will be initialized after field 'closed' [-Wreorder-ctor]
    accession_tag("<accession>", "</accession>"),
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    closed(true)
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FileEntryMaker.cpp -o FileEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c TagDetector.cpp -o TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c XmlSplitter.cpp -o XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractXmlEntries.cpp -o extractXmlEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-TagDetector.cpp -o test-100-TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.21-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)