Back to Long Tests report for BioC 3.22

This page was generated on 2025-07-12 23:55 -0400 (Sat, 12 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4783
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4520
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4564
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 6/29HostnameOS / ArchCHECK
biodbHmdb 1.15.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-07-12 09:55 -0400 (Sat, 12 Jul 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: 9920d92
git_last_commit_date: 2025-04-15 12:42:50 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  ERROR  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on nebbiolo2

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

raw results


Summary

Package: biodbHmdb
Version: 1.15.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.15.0.tar.gz
StartedAt: 2025-07-12 16:01:06 -0400 (Sat, 12 Jul 2025)
EndedAt: 2025-07-12 16:02:08 -0400 (Sat, 12 Jul 2025)
EllapsedTime: 62.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-07-12 16:02:05.344][biodb::testContext]
biodb.INFO [2025-07-12 16:02:05.346][biodb::testContext] ********************************************************************************
biodb.INFO [2025-07-12 16:02:05.347][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-07-12 16:02:05.347][biodb::testContext] ********************************************************************************
biodb.INFO [2025-07-12 16:02:05.348][biodb::testContext]
biodb.INFO [2025-07-12 16:02:05.354][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-07-12 16:02:05.356][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-07-12 16:02:05.362][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-12 16:02:05.363][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-07-12 16:02:05.364][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-07-12 16:02:05.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.368][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-07-12 16:02:05.384][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-07-12 16:02:05.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.387][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-07-12 16:02:05.388][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-07-12 16:02:05.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.392][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-07-12 16:02:05.392][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-07-12 16:02:05.393][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-07-12 16:02:05.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.397][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-07-12 16:02:05.397][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-07-12 16:02:05.398][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-07-12 16:02:05.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.402][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-07-12 16:02:05.403][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-07-12 16:02:05.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.406][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-07-12 16:02:05.407][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-07-12 16:02:05.408][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-07-12 16:02:05.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.411][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-07-12 16:02:05.412][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-07-12 16:02:05.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.415][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-07-12 16:02:05.416][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-07-12 16:02:05.417][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-07-12 16:02:05.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.420][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-07-12 16:02:05.421][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-07-12 16:02:05.422][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-07-12 16:02:05.423][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-07-12 16:02:05.424][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-07-12 16:02:05.425][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-07-12 16:02:05.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.428][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-07-12 16:02:05.429][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-07-12 16:02:05.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.432][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-07-12 16:02:05.433][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-07-12 16:02:05.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.436][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-07-12 16:02:05.437][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-07-12 16:02:05.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.440][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-07-12 16:02:05.441][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-07-12 16:02:05.442][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-07-12 16:02:05.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.446][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-07-12 16:02:05.447][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-07-12 16:02:05.450][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-07-12 16:02:05.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.453][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-07-12 16:02:05.454][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-07-12 16:02:05.455][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-07-12 16:02:05.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.461][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-07-12 16:02:05.496][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-12 16:02:05.511][self$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[2025-07-12 16:02:05.512][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.513][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-12 16:02:05.514][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.515][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-12 16:02:05.516][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-12 16:02:05.516][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-12 16:02:05.517][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-07-12 16:02:05.518][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-12 16:02:05.519][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.520][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-07-12 16:02:05.521][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-12 16:02:05.522][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:02:05.523][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.524][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-12 16:02:05.524][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-07-12 16:02:05.524][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-07-12 16:02:05.524][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-07-12 16:02:05.524][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-07-12 16:02:05.525][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-12 16:02:05.525][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:02:05.526][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:02:05.527][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-12 16:02:05.528][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:02:05.529][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:02:05.530][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-12 16:02:05.531][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:02:05.531][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-12 16:02:05.532][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-12 16:02:05.533][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-12 16:02:05.534][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:02:05.535][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-07-12 16:02:05.537][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-12 16:02:05.538][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-07-12 16:02:05.538][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.539][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-12 16:02:05.540][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.541][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-12 16:02:05.542][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-12 16:02:05.543][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-12 16:02:05.544][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-07-12 16:02:05.545][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-12 16:02:05.546][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.546][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-07-12 16:02:05.547][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-12 16:02:05.548][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:02:05.549][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.550][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-12 16:02:05.550][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-07-12 16:02:05.550][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-07-12 16:02:05.550][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-07-12 16:02:05.550][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-07-12 16:02:05.551][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-12 16:02:05.552][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:02:05.553][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:02:05.553][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-12 16:02:05.554][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:02:05.555][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:02:05.556][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-12 16:02:05.557][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:02:05.558][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-12 16:02:05.558][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-12 16:02:05.559][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-12 16:02:05.560][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:02:05.561][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-07-12 16:02:05.563][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.564][self$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[2025-07-12 16:02:05.565][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.565][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-12 16:02:05.566][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.567][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-12 16:02:05.568][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-12 16:02:05.569][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-12 16:02:05.570][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-07-12 16:02:05.571][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-12 16:02:05.572][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-07-12 16:02:05.573][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-07-12 16:02:05.573][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-12 16:02:05.574][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:02:05.575][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.576][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:02:05.577][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-12 16:02:05.578][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:02:05.579][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:02:05.580][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-12 16:02:05.580][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:02:05.581][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:02:05.582][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-12 16:02:05.583][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:02:05.584][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-12 16:02:05.585][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-12 16:02:05.585][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-12 16:02:05.586][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:02:05.587][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-07-12 16:02:05.589][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.590][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-07-12 16:02:05.591][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.592][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-12 16:02:05.593][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.593][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-12 16:02:05.594][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-12 16:02:05.595][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-12 16:02:05.596][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-07-12 16:02:05.597][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-12 16:02:05.598][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-07-12 16:02:05.599][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-07-12 16:02:05.600][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-12 16:02:05.601][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:02:05.602][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.602][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:02:05.603][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-12 16:02:05.604][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:02:05.605][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:02:05.606][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-12 16:02:05.607][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:02:05.608][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:02:05.608][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-12 16:02:05.609][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:02:05.610][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-12 16:02:05.611][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-12 16:02:05.612][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-12 16:02:05.613][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:02:05.616][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-12 16:02:05.617][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.687][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-07-12 16:02:05.691][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-07-12 16:02:05.693][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-07-12 16:02:05.694][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-07-12 16:02:05.695][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-07-12 16:02:05.696][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-07-12 16:02:05.698][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-07-12 16:02:05.699][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-07-12 16:02:05.700][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-07-12 16:02:05.702][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-07-12 16:02:05.703][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-07-12 16:02:05.704][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-07-12 16:02:05.705][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-07-12 16:02:05.707][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-07-12 16:02:05.708][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-07-12 16:02:05.709][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-07-12 16:02:05.710][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-07-12 16:02:05.712][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-07-12 16:02:05.713][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-07-12 16:02:05.714][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-07-12 16:02:05.715][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-07-12 16:02:05.717][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-07-12 16:02:05.718][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-07-12 16:02:05.719][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-07-12 16:02:05.720][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-07-12 16:02:05.722][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-07-12 16:02:05.723][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-07-12 16:02:05.724][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-07-12 16:02:05.725][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-07-12 16:02:05.727][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-07-12 16:02:05.728][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-07-12 16:02:05.729][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-07-12 16:02:05.731][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-07-12 16:02:05.732][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-07-12 16:02:05.733][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-07-12 16:02:05.734][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-07-12 16:02:05.736][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-07-12 16:02:05.737][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-07-12 16:02:05.738][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-07-12 16:02:05.739][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-07-12 16:02:05.741][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-07-12 16:02:05.742][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-07-12 16:02:05.743][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-07-12 16:02:05.745][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-07-12 16:02:05.746][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-07-12 16:02:05.747][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-07-12 16:02:05.748][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-07-12 16:02:05.750][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-07-12 16:02:05.751][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-07-12 16:02:05.752][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-07-12 16:02:05.753][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-07-12 16:02:05.755][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-07-12 16:02:05.756][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-07-12 16:02:05.757][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-07-12 16:02:05.758][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-07-12 16:02:05.760][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-07-12 16:02:05.761][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-07-12 16:02:05.762][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-07-12 16:02:05.764][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-07-12 16:02:05.765][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-07-12 16:02:05.766][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-07-12 16:02:05.767][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-07-12 16:02:05.769][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-07-12 16:02:05.770][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-07-12 16:02:05.771][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-07-12 16:02:05.772][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-07-12 16:02:05.774][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-07-12 16:02:05.775][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-07-12 16:02:05.776][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-07-12 16:02:05.778][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-07-12 16:02:05.779][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-07-12 16:02:05.780][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-07-12 16:02:05.781][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-07-12 16:02:05.783][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-07-12 16:02:05.784][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-07-12 16:02:05.789][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-07-12 16:02:05.791][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-07-12 16:02:05.792][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-07-12 16:02:05.793][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-07-12 16:02:05.794][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-07-12 16:02:05.796][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-07-12 16:02:05.797][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-07-12 16:02:05.798][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-07-12 16:02:05.804][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-07-12 16:02:05.805][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-07-12 16:02:05.808][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-12 16:02:05.809][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.811][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:05.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:05.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.820][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[2025-07-12 16:02:05.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:05.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:05.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:05.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:05.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:05.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:05.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:05.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:05.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:05.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:05.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.848][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[2025-07-12 16:02:05.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:05.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:05.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:05.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:05.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:05.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:05.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:05.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:05.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:05.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:05.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:05.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:05.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:05.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:05.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:05.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:05.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:05.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:05.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:05.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:05.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2025-07-12 16:02:05.905][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-07-12 16:02:05.924][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-07-12 16:02:05.942][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-07-12 16:02:05.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:02:05.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:05.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:05.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:05.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:05.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:05.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:02:05.950][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-07-12 16:02:05.975][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-07-12 16:02:05.977][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-12 16:02:05.978][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-07-12 16:02:05.979][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.980][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-12 16:02:05.981][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-07-12 16:02:05.982][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-07-12 16:02:05.983][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.984][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-12 16:02:05.985][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-07-12 16:02:05.986][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-12 16:02:05.987][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:05.988][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-07-12 16:02:05.990][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-12 16:02:05.991][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-07-12 16:02:05.991][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-07-12 16:02:05.991][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-07-12 16:02:05.991][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-07-12 16:02:05.991][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-07-12 16:02:05.991][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-07-12 16:02:05.991][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-07-12 16:02:05.991][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-07-12 16:02:05.991][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-07-12 16:02:05.991][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-07-12 16:02:05.991][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-07-12 16:02:05.991][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-07-12 16:02:05.991][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-07-12 16:02:05.991][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-07-12 16:02:05.991][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-07-12 16:02:05.991][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-07-12 16:02:05.991][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-07-12 16:02:05.991][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-07-12 16:02:05.992][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-12 16:02:05.993][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-12 16:02:05.993][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-07-12 16:02:05.993][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-07-12 16:02:05.994][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-07-12 16:02:05.995][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:02:05.996][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:02:05.997][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-12 16:02:05.998][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:02:05.998][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:02:05.999][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-12 16:02:06.000][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-07-12 16:02:06.000][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-07-12 16:02:06.001][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-12 16:02:06.002][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-12 16:02:06.003][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-12 16:02:06.004][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:02:06.010][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-07-12 16:02:06.012][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-07-12 16:02:06.013][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-07-12 16:02:06.015][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-07-12 16:02:06.016][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-07-12 16:02:06.038][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-07-12 16:02:06.054][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-07-12 16:02:06.061][biodb::testThat]
biodb.INFO [2025-07-12 16:02:06.062][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-07-12 16:02:06.063][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-12 16:02:06.064][biodb::testThat]
biodb.TRACE[2025-07-12 16:02:06.068][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-07-12 16:02:06.070][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-07-12 16:02:06.073][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-07-12 16:02:06.081][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-12 16:02:06.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:06.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:06.095][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:06.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:06.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:06.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-12 16:02:06.109][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.110][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.111][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.112][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.130][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.131][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.132][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.165][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.169][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.169][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.171][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.172][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.176][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:02:06.177][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:02:06.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.179][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.180][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:02:06.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:02:06.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.183][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.184][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.186][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.191][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.192][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.194][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.198][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.199][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.201][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.202][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.206][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.207][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.208][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.210][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.213][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:06.214][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:06.215][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.216][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.217][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:06.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:06.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.221][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:06.222][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:06.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.223][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.224][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:06.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:06.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.228][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:02:06.229][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:02:06.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.231][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.232][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:02:06.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:02:06.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.235][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:02:06.236][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:02:06.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.238][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.239][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:02:06.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:02:06.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.243][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:02:06.244][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:02:06.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.245][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:02:06.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:02:06.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.250][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.251][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.253][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.258][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:06.259][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:06.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.260][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:06.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:06.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.265][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-12 16:02:06.266][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-12 16:02:06.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.268][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.269][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-12 16:02:06.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-12 16:02:06.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.272][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-07-12 16:02:06.273][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-07-12 16:02:06.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.275][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.276][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-07-12 16:02:06.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-07-12 16:02:06.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.280][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-07-12 16:02:06.281][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:06.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.282][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.284][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-07-12 16:02:06.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:06.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.331][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.335][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.338][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.342][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:02:06.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:02:06.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.346][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:02:06.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:02:06.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.349][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:02:06.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:02:06.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.374][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:06.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:06.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.378][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:06.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:06.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.382][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:06.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:06.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.385][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:06.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:06.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.389][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:06.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:06.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.392][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:06.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:06.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.396][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:06.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:06.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.400][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:06.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:06.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.403][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:06.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:06.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.407][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-12 16:02:06.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-12 16:02:06.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.414][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-12 16:02:06.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-12 16:02:06.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.417][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-12 16:02:06.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-12 16:02:06.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.421][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:02:06.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:02:06.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.424][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:02:06.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:02:06.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.428][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:02:06.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:02:06.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.432][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:02:06.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:02:06.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:02:06.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:02:06.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.439][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:02:06.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:02:06.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.442][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:02:06.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:02:06.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.446][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:02:06.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:02:06.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.449][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:02:06.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:02:06.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.453][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.456][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.460][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.474][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:06.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:06.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.478][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:06.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:06.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.482][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:06.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:06.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.485][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.489][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.492][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.496][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.499][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.503][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.507][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-07-12 16:02:06.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-07-12 16:02:06.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.510][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-07-12 16:02:06.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-07-12 16:02:06.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.514][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-07-12 16:02:06.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-07-12 16:02:06.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.517][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-07-12 16:02:06.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:02:06.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.521][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:02:06.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:02:06.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.525][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:02:06.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:02:06.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.528][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:02:06.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:02:06.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.532][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-07-12 16:02:06.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:02:06.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:06.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:06.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.590][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:06.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:06.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.593][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:06.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:06.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.597][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:06.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:06.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.600][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:06.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:06.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.604][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-07-12 16:02:06.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-07-12 16:02:06.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.608][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-07-12 16:02:06.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-07-12 16:02:06.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.615][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-07-12 16:02:06.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-07-12 16:02:06.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-12 16:02:06.640][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-07-12 16:02:06.642][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-12 16:02:06.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-12 16:02:06.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.646][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-12 16:02:06.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-12 16:02:06.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.649][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-12 16:02:06.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-12 16:02:06.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.653][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-12 16:02:06.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-12 16:02:06.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.665][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-07-12 16:02:06.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-07-12 16:02:06.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.698][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-07-12 16:02:06.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-07-12 16:02:06.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.702][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-07-12 16:02:06.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-07-12 16:02:06.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.705][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-07-12 16:02:06.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-07-12 16:02:06.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.725][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.726][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.728][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:06.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:06.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.739][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.742][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.746][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.750][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.751][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.752][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.753][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:06.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.773][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.774][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.776][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:06.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.786][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.790][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.794][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.797][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.798][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.800][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.801][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:06.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.824][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.826][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.827][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.828][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-07-12 16:02:06.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.838][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.841][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.845][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.849][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.849][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.850][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.851][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.852][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:06.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.862][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:06.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:06.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.865][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:06.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:06.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.869][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:06.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:06.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.872][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:06.873][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:06.874][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.875][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.876][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:06.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:06.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.885][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-12 16:02:06.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-12 16:02:06.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.889][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-12 16:02:06.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-12 16:02:06.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.892][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-12 16:02:06.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-12 16:02:06.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.896][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-12 16:02:06.897][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-12 16:02:06.898][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.899][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.900][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-12 16:02:06.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-12 16:02:06.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.909][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:02:06.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:02:06.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.913][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:02:06.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:02:06.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.916][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:02:06.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:02:06.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.920][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:02:06.921][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:02:06.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.923][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.923][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:02:06.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:02:06.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.933][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.937][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.940][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.944][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.945][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.950][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.951][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-12 16:02:06.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.971][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.972][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.974][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:06.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.984][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:06.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:06.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.988][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:06.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:06.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.991][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:06.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:06.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.995][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:06.996][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:06.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:06.998][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:06.999][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:07.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:07.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.008][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:07.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:07.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.012][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:07.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:07.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.015][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:07.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:07.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.019][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:07.020][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:07.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.022][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.023][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:07.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:07.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.032][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:07.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:07.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.036][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:07.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:07.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.039][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:07.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:07.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.043][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:07.044][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:07.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.045][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.046][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:07.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:07.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.056][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-07-12 16:02:07.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-07-12 16:02:07.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.059][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-07-12 16:02:07.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-07-12 16:02:07.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.063][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-07-12 16:02:07.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-07-12 16:02:07.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.067][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-07-12 16:02:07.068][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-07-12 16:02:07.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.069][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.070][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-07-12 16:02:07.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-07-12 16:02:07.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.083][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:02:07.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:02:07.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.087][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:02:07.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:02:07.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.090][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:02:07.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:02:07.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.094][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:02:07.095][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:02:07.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.097][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.098][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:02:07.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:02:07.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.107][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:02:07.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:02:07.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.111][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:02:07.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:02:07.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.114][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:02:07.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:02:07.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.118][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:02:07.119][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:02:07.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.120][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.121][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:02:07.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:02:07.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.131][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:02:07.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:02:07.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.135][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:02:07.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:02:07.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.138][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:02:07.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:02:07.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.142][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:02:07.143][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:02:07.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.144][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.145][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:02:07.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:02:07.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.155][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:02:07.156][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:02:07.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.158][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.161][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-12 16:02:07.162][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-12 16:02:07.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.164][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.168][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:02:07.169][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:02:07.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.171][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.174][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-07-12 16:02:07.175][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-07-12 16:02:07.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.177][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.181][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:07.182][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-07-12 16:02:07.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.183][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.187][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:07.188][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-12 16:02:07.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.190][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.193][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:07.194][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-12 16:02:07.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.200][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.203][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:07.204][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-07-12 16:02:07.205][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.206][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.210][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-12 16:02:07.211][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-12 16:02:07.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.212][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.216][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:02:07.217][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:02:07.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.219][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.222][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:02:07.223][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:02:07.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.225][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.229][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:02:07.230][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:02:07.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.231][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.235][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:07.236][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-07-12 16:02:07.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.238][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.241][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:07.242][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-12 16:02:07.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.244][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.248][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:07.248][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:07.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.250][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.254][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:07.255][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-12 16:02:07.256][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.257][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.260][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:07.261][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:07.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.263][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.266][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-07-12 16:02:07.267][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-07-12 16:02:07.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.269][ef$get] fields variable is a list.
biodb.INFO [2025-07-12 16:02:07.275][biodb::testThat]
biodb.INFO [2025-07-12 16:02:07.276][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-07-12 16:02:07.277][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-12 16:02:07.278][biodb::testThat]
biodb.DEBUG[2025-07-12 16:02:07.291][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-07-12 16:02:07.293][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-07-12 16:02:07.296][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-07-12 16:02:07.326][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-07-12 16:02:07.328][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-07-12 16:02:07.328][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-07-12 16:02:07.362][biodb::testThat]
biodb.INFO [2025-07-12 16:02:07.363][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-07-12 16:02:07.364][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-12 16:02:07.365][biodb::testThat]
biodb.TRACE[2025-07-12 16:02:07.368][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:07.369][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:07.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.370][ef$get] fields variable is a list.
biodb.DEBUG[2025-07-12 16:02:07.372][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-07-12 16:02:07.390][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-07-12 16:02:07.437][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-07-12 16:02:07.439][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-07-12 16:02:07.440][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-07-12 16:02:07.441][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-07-12 16:02:07.453][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-07-12 16:02:07.474][biodb::testThat]
biodb.INFO [2025-07-12 16:02:07.475][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-07-12 16:02:07.476][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-12 16:02:07.477][biodb::testThat]
biodb.DEBUG[2025-07-12 16:02:07.483][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-07-12 16:02:07.484][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-07-12 16:02:07.485][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-07-12 16:02:07.487][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-07-12 16:02:07.488][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-07-12 16:02:07.489][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-07-12 16:02:07.500][biodb::testThat]
biodb.INFO [2025-07-12 16:02:07.501][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-07-12 16:02:07.502][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-12 16:02:07.503][biodb::testThat]
biodb.DEBUG[2025-07-12 16:02:07.506][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-07-12 16:02:07.507][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-07-12 16:02:07.508][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-07-12 16:02:07.509][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-07-12 16:02:07.510][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-07-12 16:02:07.511][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-07-12 16:02:07.523][biodb::testThat]
biodb.INFO [2025-07-12 16:02:07.524][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-07-12 16:02:07.525][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-12 16:02:07.526][biodb::testThat]
biodb.INFO [2025-07-12 16:02:07.538][biodb::testThat]
biodb.INFO [2025-07-12 16:02:07.539][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-07-12 16:02:07.544][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-12 16:02:07.544][biodb::testThat]
biodb.INFO [2025-07-12 16:02:07.557][biodb::testThat]
biodb.INFO [2025-07-12 16:02:07.558][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-07-12 16:02:07.558][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-12 16:02:07.559][biodb::testThat]
biodb.INFO [2025-07-12 16:02:07.572][biodb::testThat]
biodb.INFO [2025-07-12 16:02:07.573][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-07-12 16:02:07.573][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-12 16:02:07.574][biodb::testThat]
biodb.TRACE[2025-07-12 16:02:07.599][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:07.600][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:07.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.602][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.603][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-12 16:02:07.604][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-12 16:02:07.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.605][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.606][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:07.607][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:07.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.609][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.610][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:02:07.611][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:02:07.612][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.612][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.613][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-12 16:02:07.614][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-12 16:02:07.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.616][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:02:07.617][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:07.618][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-07-12 16:02:07.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:02:07.619][ef$get] fields variable is a list.
biodb.INFO [2025-07-12 16:02:07.620][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-07-12 16:02:07.621][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-07-12 16:02:07.622][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-07-12 16:02:07.623][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:02:07.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:02:07.625][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:02:07.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:02:07.626][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:02:07.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
   5.       └─base::vapply(id, fct, FUN.VALUE = "")
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  
  [ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log’
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.15.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor ‘EntryMaker::EntryMaker()’:
EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** 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)