Back to Long Tests report for BioC 3.22

This page was generated on 2025-06-14 23:55 -0400 (Sat, 14 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4807
palomino8Windows Server 2022 Datacenterx644.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" 4548
lconwaymacOS 12.7.1 Montereyx86_644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4586
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: 2025-06-14 09:55 -0400 (Sat, 14 Jun 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  NA  

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: 2025-06-14 16:01:10 -0400 (Sat, 14 Jun 2025)
EndedAt: 2025-06-14 16:02:12 -0400 (Sat, 14 Jun 2025)
EllapsedTime: 62.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-06-14 16:02:08.791][biodb::testContext]
biodb.INFO [2025-06-14 16:02:08.792][biodb::testContext] ********************************************************************************
biodb.INFO [2025-06-14 16:02:08.793][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-06-14 16:02:08.794][biodb::testContext] ********************************************************************************
biodb.INFO [2025-06-14 16:02:08.795][biodb::testContext]
biodb.INFO [2025-06-14 16:02:08.801][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-06-14 16:02:08.803][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-06-14 16:02:08.809][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-14 16:02:08.810][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-06-14 16:02:08.811][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-06-14 16:02:08.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:08.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:08.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:08.814][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-06-14 16:02:08.831][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-06-14 16:02:08.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:08.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:08.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:08.834][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-06-14 16:02:08.835][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-06-14 16:02:08.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:08.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:08.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:08.838][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-06-14 16:02:08.839][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-06-14 16:02:08.840][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-06-14 16:02:08.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:08.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:08.843][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[2025-06-14 16:02:08.844][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-06-14 16:02:08.844][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-06-14 16:02:08.845][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-06-14 16:02:08.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:08.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:08.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:08.849][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-06-14 16:02:08.850][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-06-14 16:02:08.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:08.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:08.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:08.853][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-06-14 16:02:08.854][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-06-14 16:02:08.855][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-06-14 16:02:08.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:08.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:08.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:08.858][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-06-14 16:02:08.859][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-06-14 16:02:08.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:08.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:08.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:08.862][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-06-14 16:02:08.863][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-06-14 16:02:08.864][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-06-14 16:02:08.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:08.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:08.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:08.867][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-06-14 16:02:08.868][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-06-14 16:02:08.869][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-06-14 16:02:08.870][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-06-14 16:02:08.871][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-06-14 16:02:08.872][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-06-14 16:02:08.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:08.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:08.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:08.875][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-06-14 16:02:08.876][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-06-14 16:02:08.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:08.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:08.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:08.879][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-06-14 16:02:08.880][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-06-14 16:02:08.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:08.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:08.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:08.884][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-06-14 16:02:08.884][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-06-14 16:02:08.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:08.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:08.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:08.888][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-06-14 16:02:08.889][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-06-14 16:02:08.890][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-06-14 16:02:08.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:08.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:08.892][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[2025-06-14 16:02:08.893][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-06-14 16:02:08.894][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-06-14 16:02:08.897][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-06-14 16:02:08.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:08.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:08.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:08.900][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-06-14 16:02:08.901][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-06-14 16:02:08.902][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-06-14 16:02:08.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:08.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:08.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:08.908][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-06-14 16:02:08.944][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-14 16:02:08.959][self$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[2025-06-14 16:02:08.960][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:08.961][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-14 16:02:08.962][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:08.963][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-14 16:02:08.964][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-14 16:02:08.965][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-14 16:02:08.966][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-06-14 16:02:08.967][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-14 16:02:08.967][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:08.968][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-06-14 16:02:08.969][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-14 16:02:08.970][self$setPropertyValue]
biodb.DEBUG[2025-06-14 16:02:08.971][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:08.972][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-14 16:02:08.972][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-14 16:02:08.972][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-14 16:02:08.972][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-06-14 16:02:08.972][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-06-14 16:02:08.973][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-14 16:02:08.974][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-14 16:02:08.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-14 16:02:08.976][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-14 16:02:08.976][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-14 16:02:08.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-14 16:02:08.978][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-14 16:02:08.979][self$setPropertyValue]
biodb.DEBUG[2025-06-14 16:02:08.980][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-14 16:02:08.981][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-14 16:02:08.982][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-14 16:02:08.982][self$setPropertyValue]
biodb.DEBUG[2025-06-14 16:02:08.983][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-06-14 16:02:08.985][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-14 16:02:08.986][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-06-14 16:02:08.987][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:08.988][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-14 16:02:08.989][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:08.990][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-14 16:02:08.990][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-14 16:02:08.991][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-14 16:02:08.992][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-06-14 16:02:08.993][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-14 16:02:08.994][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:08.995][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-06-14 16:02:08.996][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-14 16:02:08.997][self$setPropertyValue]
biodb.DEBUG[2025-06-14 16:02:08.998][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:08.999][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-14 16:02:08.999][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-14 16:02:08.999][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-14 16:02:08.999][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-06-14 16:02:08.999][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-06-14 16:02:08.999][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-14 16:02:09.000][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-14 16:02:09.001][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-14 16:02:09.002][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-14 16:02:09.003][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-14 16:02:09.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-14 16:02:09.005][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-14 16:02:09.005][self$setPropertyValue]
biodb.DEBUG[2025-06-14 16:02:09.006][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-14 16:02:09.007][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-14 16:02:09.008][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-14 16:02:09.009][self$setPropertyValue]
biodb.DEBUG[2025-06-14 16:02:09.010][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-06-14 16:02:09.011][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:09.012][self$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[2025-06-14 16:02:09.013][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:09.014][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-14 16:02:09.015][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:09.016][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-14 16:02:09.017][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-14 16:02:09.018][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-14 16:02:09.019][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-06-14 16:02:09.020][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-14 16:02:09.020][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-06-14 16:02:09.021][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-06-14 16:02:09.022][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-14 16:02:09.023][self$setPropertyValue]
biodb.DEBUG[2025-06-14 16:02:09.024][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:09.025][self$setPropertyValue]
biodb.DEBUG[2025-06-14 16:02:09.026][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-14 16:02:09.027][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-14 16:02:09.027][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-14 16:02:09.028][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-14 16:02:09.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-14 16:02:09.030][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-14 16:02:09.031][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-14 16:02:09.032][self$setPropertyValue]
biodb.DEBUG[2025-06-14 16:02:09.033][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-14 16:02:09.033][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-14 16:02:09.034][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-14 16:02:09.035][self$setPropertyValue]
biodb.DEBUG[2025-06-14 16:02:09.036][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-06-14 16:02:09.038][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:09.039][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-06-14 16:02:09.040][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:09.041][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-14 16:02:09.041][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:09.042][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-14 16:02:09.043][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-14 16:02:09.044][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-14 16:02:09.045][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-06-14 16:02:09.046][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-14 16:02:09.047][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-06-14 16:02:09.048][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-06-14 16:02:09.049][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-14 16:02:09.050][self$setPropertyValue]
biodb.DEBUG[2025-06-14 16:02:09.050][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:09.051][self$setPropertyValue]
biodb.DEBUG[2025-06-14 16:02:09.052][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-14 16:02:09.053][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-14 16:02:09.054][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-14 16:02:09.055][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-14 16:02:09.056][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-14 16:02:09.056][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-14 16:02:09.057][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-14 16:02:09.058][self$setPropertyValue]
biodb.DEBUG[2025-06-14 16:02:09.059][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-14 16:02:09.060][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-14 16:02:09.061][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-14 16:02:09.062][self$setPropertyValue]
biodb.DEBUG[2025-06-14 16:02:09.065][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-14 16:02:09.066][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.136][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-06-14 16:02:09.141][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-06-14 16:02:09.142][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-06-14 16:02:09.143][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-06-14 16:02:09.145][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-06-14 16:02:09.146][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-06-14 16:02:09.147][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-06-14 16:02:09.148][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-06-14 16:02:09.150][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-06-14 16:02:09.151][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-06-14 16:02:09.152][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-06-14 16:02:09.153][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-06-14 16:02:09.155][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-06-14 16:02:09.156][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-06-14 16:02:09.157][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-06-14 16:02:09.159][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-06-14 16:02:09.160][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-06-14 16:02:09.161][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-06-14 16:02:09.162][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-06-14 16:02:09.164][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-06-14 16:02:09.165][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-06-14 16:02:09.166][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-06-14 16:02:09.167][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-06-14 16:02:09.169][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-06-14 16:02:09.170][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-06-14 16:02:09.171][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-06-14 16:02:09.172][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-06-14 16:02:09.174][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-06-14 16:02:09.175][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-06-14 16:02:09.176][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-06-14 16:02:09.178][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-06-14 16:02:09.179][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-06-14 16:02:09.180][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-06-14 16:02:09.181][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-06-14 16:02:09.183][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-06-14 16:02:09.184][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-06-14 16:02:09.185][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-06-14 16:02:09.186][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-06-14 16:02:09.188][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-06-14 16:02:09.189][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-06-14 16:02:09.190][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-06-14 16:02:09.191][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-06-14 16:02:09.193][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-06-14 16:02:09.194][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-06-14 16:02:09.195][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-06-14 16:02:09.196][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-06-14 16:02:09.198][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-06-14 16:02:09.199][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-06-14 16:02:09.200][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-06-14 16:02:09.202][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-06-14 16:02:09.203][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-06-14 16:02:09.204][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-06-14 16:02:09.205][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-06-14 16:02:09.207][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-06-14 16:02:09.208][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-06-14 16:02:09.209][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-06-14 16:02:09.210][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-06-14 16:02:09.212][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-06-14 16:02:09.213][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-06-14 16:02:09.214][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-06-14 16:02:09.215][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-06-14 16:02:09.217][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-06-14 16:02:09.218][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-06-14 16:02:09.219][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-06-14 16:02:09.220][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-06-14 16:02:09.222][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-06-14 16:02:09.223][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-06-14 16:02:09.224][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-06-14 16:02:09.225][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-06-14 16:02:09.227][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-06-14 16:02:09.228][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-06-14 16:02:09.229][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-06-14 16:02:09.231][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-06-14 16:02:09.232][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-06-14 16:02:09.237][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-06-14 16:02:09.238][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-06-14 16:02:09.239][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-06-14 16:02:09.241][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-06-14 16:02:09.242][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-06-14 16:02:09.243][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-06-14 16:02:09.244][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-06-14 16:02:09.246][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-06-14 16:02:09.247][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-06-14 16:02:09.252][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-06-14 16:02:09.254][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-06-14 16:02:09.257][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-14 16:02:09.258][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.259][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:09.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:09.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:09.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:09.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:09.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:09.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:09.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:09.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:09.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:09.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:09.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:09.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:09.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:09.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:09.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:09.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:09.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:09.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:09.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:09.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:09.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:09.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:09.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:09.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:09.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:09.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:09.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:09.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:09.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:09.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:09.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:09.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.353][FUN] Functions in observer BiodbConfig: [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 [2025-06-14 16:02:09.354][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-06-14 16:02:09.363][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-06-14 16:02:09.375][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-06-14 16:02:09.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-14 16:02:09.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:09.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:09.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-14 16:02:09.383][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-06-14 16:02:09.414][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-06-14 16:02:09.416][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-14 16:02:09.417][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-06-14 16:02:09.418][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:09.419][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-14 16:02:09.420][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-06-14 16:02:09.421][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-06-14 16:02:09.422][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:09.423][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-14 16:02:09.424][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-06-14 16:02:09.425][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-14 16:02:09.426][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:09.427][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-06-14 16:02:09.428][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-14 16:02:09.429][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-06-14 16:02:09.429][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-06-14 16:02:09.429][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-06-14 16:02:09.429][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-06-14 16:02:09.429][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-06-14 16:02:09.429][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-06-14 16:02:09.429][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-06-14 16:02:09.429][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-06-14 16:02:09.429][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-06-14 16:02:09.429][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-06-14 16:02:09.429][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-06-14 16:02:09.429][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-06-14 16:02:09.429][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-06-14 16:02:09.429][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-06-14 16:02:09.429][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-06-14 16:02:09.429][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-06-14 16:02:09.429][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-06-14 16:02:09.429][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-06-14 16:02:09.431][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-14 16:02:09.432][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-14 16:02:09.432][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-06-14 16:02:09.432][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-06-14 16:02:09.433][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-06-14 16:02:09.434][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-14 16:02:09.435][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-14 16:02:09.435][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-14 16:02:09.436][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-14 16:02:09.437][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-14 16:02:09.438][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-14 16:02:09.439][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-06-14 16:02:09.439][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-06-14 16:02:09.440][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-14 16:02:09.441][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-14 16:02:09.442][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-14 16:02:09.443][self$setPropertyValue]
biodb.DEBUG[2025-06-14 16:02:09.449][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-06-14 16:02:09.451][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-06-14 16:02:09.452][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-06-14 16:02:09.454][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-06-14 16:02:09.455][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-06-14 16:02:09.477][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-06-14 16:02:09.492][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-06-14 16:02:09.500][biodb::testThat]
biodb.INFO [2025-06-14 16:02:09.501][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-06-14 16:02:09.502][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-14 16:02:09.503][biodb::testThat]
biodb.TRACE[2025-06-14 16:02:09.506][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[2025-06-14 16:02:09.508][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-06-14 16:02:09.511][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-06-14 16:02:09.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-14 16:02:09.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:09.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:09.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:09.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:09.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:09.536][FUN] Functions in observer BiodbConfig: [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[2025-06-14 16:02:09.547][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:09.548][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:09.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.550][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:09.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:09.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.568][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:09.569][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:09.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.571][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.606][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:09.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:09.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.610][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-06-14 16:02:09.611][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-06-14 16:02:09.612][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.613][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.614][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-06-14 16:02:09.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-06-14 16:02:09.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.618][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-06-14 16:02:09.619][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-06-14 16:02:09.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.620][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.622][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-06-14 16:02:09.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-06-14 16:02:09.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.625][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-14 16:02:09.626][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-14 16:02:09.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.628][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-14 16:02:09.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-14 16:02:09.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.633][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:09.634][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:09.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.635][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:09.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:09.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.640][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:09.641][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:09.642][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.643][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.644][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:09.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:09.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.648][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:09.649][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:09.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.651][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.652][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:09.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:09.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.655][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:09.656][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:09.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.658][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.659][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:09.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:09.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.663][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:09.664][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:09.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.666][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.667][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:09.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:09.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.671][ef$get] Asked field names are: formula.
biodb.TRACE[2025-06-14 16:02:09.672][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-14 16:02:09.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.673][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.674][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-14 16:02:09.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-14 16:02:09.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.678][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-06-14 16:02:09.679][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-14 16:02:09.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.681][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.682][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-14 16:02:09.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-14 16:02:09.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.686][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-14 16:02:09.687][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-14 16:02:09.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.688][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.689][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-14 16:02:09.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-14 16:02:09.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.693][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:09.694][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:09.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.696][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:09.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:09.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.701][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:09.702][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:09.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.703][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.704][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:09.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:09.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.708][ef$get] Asked field names are: description.
biodb.TRACE[2025-06-14 16:02:09.709][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-06-14 16:02:09.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.711][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.712][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-06-14 16:02:09.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-06-14 16:02:09.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.716][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-06-14 16:02:09.717][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-14 16:02:09.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.718][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.720][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-06-14 16:02:09.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-14 16:02:09.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.723][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-06-14 16:02:09.724][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:09.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.726][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.727][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-06-14 16:02:09.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:09.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:09.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:09.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:09.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:09.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:09.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:09.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.776][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-06-14 16:02:09.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-06-14 16:02:09.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.780][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-06-14 16:02:09.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-06-14 16:02:09.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.784][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-06-14 16:02:09.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-06-14 16:02:09.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.788][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-06-14 16:02:09.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-06-14 16:02:09.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.791][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-06-14 16:02:09.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-06-14 16:02:09.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.795][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-06-14 16:02:09.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-06-14 16:02:09.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-14 16:02:09.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-14 16:02:09.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-14 16:02:09.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-14 16:02:09.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-14 16:02:09.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-14 16:02:09.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:09.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:09.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:09.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:09.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:09.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:09.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.820][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:09.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:09.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.824][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:09.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:09.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.827][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:09.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:09.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.831][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:09.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:09.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.835][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:09.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:09.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.838][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:09.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:09.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.842][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:09.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:09.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.846][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:09.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:09.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.849][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:09.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:09.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.853][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-06-14 16:02:09.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-06-14 16:02:09.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.860][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-06-14 16:02:09.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-06-14 16:02:09.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.864][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-06-14 16:02:09.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-06-14 16:02:09.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.867][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-14 16:02:09.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-14 16:02:09.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.871][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-14 16:02:09.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-14 16:02:09.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.875][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-14 16:02:09.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-14 16:02:09.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.878][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-14 16:02:09.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-14 16:02:09.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.882][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-14 16:02:09.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-14 16:02:09.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.885][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-14 16:02:09.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-14 16:02:09.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.889][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-14 16:02:09.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-14 16:02:09.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-14 16:02:09.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-14 16:02:09.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.896][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-14 16:02:09.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-14 16:02:09.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.900][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:09.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:09.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.904][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:09.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:09.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.907][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:09.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:09.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:09.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:09.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:09.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:09.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:09.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:09.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.922][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:09.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:09.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.926][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:09.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:09.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.929][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:09.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:09.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.933][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:09.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:09.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.937][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:09.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:09.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.940][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:09.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:09.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.944][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:09.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:09.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.947][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:09.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:09.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.951][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:09.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:09.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.955][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-06-14 16:02:09.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-14 16:02:09.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.958][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-06-14 16:02:09.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-14 16:02:09.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.962][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-06-14 16:02:09.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-14 16:02:09.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.966][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-06-14 16:02:09.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-14 16:02:09.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.970][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-14 16:02:09.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-14 16:02:09.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.973][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-14 16:02:09.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-14 16:02:09.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.977][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-14 16:02:09.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-14 16:02:09.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:09.981][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-06-14 16:02:09.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-14 16:02:09.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:09.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.035][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:10.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:10.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.039][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:10.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:10.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.043][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:10.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:10.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.046][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:10.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:10.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.050][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:10.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:10.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.054][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-06-14 16:02:10.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-06-14 16:02:10.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.057][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-06-14 16:02:10.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-06-14 16:02:10.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.064][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-06-14 16:02:10.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-06-14 16:02:10.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-06-14 16:02:10.090][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-06-14 16:02:10.092][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-06-14 16:02:10.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-06-14 16:02:10.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.096][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-06-14 16:02:10.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-06-14 16:02:10.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.099][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-06-14 16:02:10.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-06-14 16:02:10.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.103][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-06-14 16:02:10.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-06-14 16:02:10.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.115][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-06-14 16:02:10.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-06-14 16:02:10.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.149][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-06-14 16:02:10.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-06-14 16:02:10.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.152][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-06-14 16:02:10.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-06-14 16:02:10.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.156][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-06-14 16:02:10.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-06-14 16:02:10.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.176][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.177][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.179][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.190][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:10.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:10.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.194][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:10.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:10.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.198][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:10.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:10.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.201][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:10.202][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:10.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.204][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.205][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:10.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:10.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:10.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:10.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:10.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:10.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:10.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:10.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.226][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:10.227][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:10.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.229][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:10.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:10.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.239][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:10.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:10.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.243][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:10.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:10.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.247][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:10.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:10.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.250][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:10.251][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:10.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.253][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.254][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:10.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:10.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-14 16:02:10.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-14 16:02:10.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-14 16:02:10.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-14 16:02:10.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-14 16:02:10.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-14 16:02:10.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.278][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-14 16:02:10.279][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-14 16:02:10.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.281][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-14 16:02:10.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-14 16:02:10.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.292][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:10.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:10.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.296][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:10.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:10.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.299][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:10.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:10.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.303][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:10.304][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:10.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.305][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.306][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:10.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:10.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.316][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:10.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:10.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.320][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:10.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:10.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.323][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:10.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:10.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.327][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:10.328][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:10.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.330][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.331][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:10.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:10.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.340][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-06-14 16:02:10.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-06-14 16:02:10.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.344][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-06-14 16:02:10.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-06-14 16:02:10.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.348][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-06-14 16:02:10.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-06-14 16:02:10.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.351][ef$get] Asked field names are: description.
biodb.TRACE[2025-06-14 16:02:10.352][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-06-14 16:02:10.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.354][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.355][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-06-14 16:02:10.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-06-14 16:02:10.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.365][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-14 16:02:10.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-14 16:02:10.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.368][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-14 16:02:10.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-14 16:02:10.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.372][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-14 16:02:10.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-14 16:02:10.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.375][ef$get] Asked field names are: formula.
biodb.TRACE[2025-06-14 16:02:10.376][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-14 16:02:10.377][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.378][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.379][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-14 16:02:10.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-14 16:02:10.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.389][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-06-14 16:02:10.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-06-14 16:02:10.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.392][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-06-14 16:02:10.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-06-14 16:02:10.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.396][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-06-14 16:02:10.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-06-14 16:02:10.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.400][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-06-14 16:02:10.401][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-06-14 16:02:10.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.406][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.407][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-06-14 16:02:10.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-06-14 16:02:10.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:10.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:10.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:10.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:10.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:10.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:10.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.427][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:10.428][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:10.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.430][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:10.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:10.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.441][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:10.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:10.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.444][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:10.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:10.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.448][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:10.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:10.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.451][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:10.452][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:10.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.454][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.455][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:10.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:10.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.465][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:10.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:10.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.468][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:10.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:10.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.472][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:10.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:10.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.475][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:10.476][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:10.477][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.478][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.479][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:10.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:10.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.489][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:10.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:10.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.492][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:10.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:10.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.496][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:10.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:10.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.499][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:10.500][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:10.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.502][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.503][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:10.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:10.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.513][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-06-14 16:02:10.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-14 16:02:10.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.516][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-06-14 16:02:10.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-14 16:02:10.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.520][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-06-14 16:02:10.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-14 16:02:10.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.523][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-06-14 16:02:10.524][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-14 16:02:10.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.526][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.527][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-06-14 16:02:10.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-14 16:02:10.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.540][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-14 16:02:10.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-14 16:02:10.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-14 16:02:10.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-14 16:02:10.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.548][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-14 16:02:10.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-14 16:02:10.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.551][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-06-14 16:02:10.552][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-14 16:02:10.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.554][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.555][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-14 16:02:10.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-14 16:02:10.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.565][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-14 16:02:10.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-14 16:02:10.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-14 16:02:10.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-14 16:02:10.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.572][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-14 16:02:10.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-14 16:02:10.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.576][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-14 16:02:10.576][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-14 16:02:10.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.578][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.579][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-14 16:02:10.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-14 16:02:10.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.589][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-06-14 16:02:10.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-06-14 16:02:10.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.593][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-06-14 16:02:10.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-06-14 16:02:10.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.596][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-06-14 16:02:10.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-06-14 16:02:10.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.600][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-06-14 16:02:10.601][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-06-14 16:02:10.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.603][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.604][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-06-14 16:02:10.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-06-14 16:02:10.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.613][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-14 16:02:10.614][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-14 16:02:10.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.616][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.620][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-06-14 16:02:10.621][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-06-14 16:02:10.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.623][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.626][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-06-14 16:02:10.627][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-06-14 16:02:10.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.629][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.633][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-06-14 16:02:10.634][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-06-14 16:02:10.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.635][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.639][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:10.640][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-06-14 16:02:10.641][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.642][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.645][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:10.646][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-14 16:02:10.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.648][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.652][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:10.653][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-14 16:02:10.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.658][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.662][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:10.663][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-06-14 16:02:10.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.665][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.669][ef$get] Asked field names are: description.
biodb.TRACE[2025-06-14 16:02:10.670][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-06-14 16:02:10.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.671][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.675][ef$get] Asked field names are: formula.
biodb.TRACE[2025-06-14 16:02:10.676][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-14 16:02:10.677][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.678][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.681][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-06-14 16:02:10.682][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-14 16:02:10.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.684][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.688][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-14 16:02:10.689][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-14 16:02:10.690][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.690][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.694][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:10.695][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-06-14 16:02:10.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.697][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.700][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:10.702][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-14 16:02:10.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.703][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.707][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:10.708][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:10.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.710][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.713][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:10.714][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-14 16:02:10.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.716][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.720][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:10.721][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:10.722][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.723][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:10.726][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-06-14 16:02:10.727][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-06-14 16:02:10.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.729][ef$get] fields variable is a list.
biodb.INFO [2025-06-14 16:02:10.735][biodb::testThat]
biodb.INFO [2025-06-14 16:02:10.736][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-06-14 16:02:10.737][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-14 16:02:10.738][biodb::testThat]
biodb.DEBUG[2025-06-14 16:02:10.751][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-06-14 16:02:10.753][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-06-14 16:02:10.756][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-06-14 16:02:10.787][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-06-14 16:02:10.788][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-06-14 16:02:10.789][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-06-14 16:02:10.824][biodb::testThat]
biodb.INFO [2025-06-14 16:02:10.825][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-06-14 16:02:10.826][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-14 16:02:10.827][biodb::testThat]
biodb.TRACE[2025-06-14 16:02:10.829][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:10.830][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:10.831][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:10.832][ef$get] fields variable is a list.
biodb.DEBUG[2025-06-14 16:02:10.833][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-06-14 16:02:10.853][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-06-14 16:02:10.901][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-06-14 16:02:10.903][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-06-14 16:02:10.904][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-06-14 16:02:10.905][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-06-14 16:02:10.917][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-06-14 16:02:10.939][biodb::testThat]
biodb.INFO [2025-06-14 16:02:10.940][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-06-14 16:02:10.941][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-14 16:02:10.942][biodb::testThat]
biodb.DEBUG[2025-06-14 16:02:10.948][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-06-14 16:02:10.949][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-06-14 16:02:10.951][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-06-14 16:02:10.952][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-06-14 16:02:10.953][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-06-14 16:02:10.954][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-06-14 16:02:10.966][biodb::testThat]
biodb.INFO [2025-06-14 16:02:10.966][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-06-14 16:02:10.967][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-14 16:02:10.968][biodb::testThat]
biodb.DEBUG[2025-06-14 16:02:10.972][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-06-14 16:02:10.972][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-06-14 16:02:10.974][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-06-14 16:02:10.975][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-06-14 16:02:10.976][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-06-14 16:02:10.977][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-06-14 16:02:10.989][biodb::testThat]
biodb.INFO [2025-06-14 16:02:10.990][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-06-14 16:02:10.991][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-14 16:02:10.991][biodb::testThat]
biodb.INFO [2025-06-14 16:02:11.004][biodb::testThat]
biodb.INFO [2025-06-14 16:02:11.009][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-06-14 16:02:11.010][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-14 16:02:11.010][biodb::testThat]
biodb.INFO [2025-06-14 16:02:11.023][biodb::testThat]
biodb.INFO [2025-06-14 16:02:11.024][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-06-14 16:02:11.024][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-14 16:02:11.025][biodb::testThat]
biodb.INFO [2025-06-14 16:02:11.038][biodb::testThat]
biodb.INFO [2025-06-14 16:02:11.038][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-06-14 16:02:11.039][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-14 16:02:11.040][biodb::testThat]
biodb.TRACE[2025-06-14 16:02:11.065][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:11.066][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:11.067][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:11.068][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:11.069][ef$get] Asked field names are: description.
biodb.TRACE[2025-06-14 16:02:11.069][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-06-14 16:02:11.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:11.071][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:11.072][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:11.073][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:11.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:11.075][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:11.076][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-14 16:02:11.077][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-14 16:02:11.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:11.078][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:11.079][ef$get] Asked field names are: description.
biodb.TRACE[2025-06-14 16:02:11.080][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-06-14 16:02:11.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:11.082][ef$get] fields variable is a list.
biodb.TRACE[2025-06-14 16:02:11.083][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:11.084][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-06-14 16:02:11.085][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-14 16:02:11.086][ef$get] fields variable is a list.
biodb.INFO [2025-06-14 16:02:11.087][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-06-14 16:02:11.088][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-06-14 16:02:11.088][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-06-14 16:02:11.089][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-14 16:02:11.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-14 16:02:11.091][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-14 16:02:11.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-14 16:02:11.092][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-06-14 16:02:11.093][FUN] Functions in observer 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 4.5.0 (2025-04-11)
* 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)