Back to Long Tests report for BioC 3.22

This page was generated on 2025-12-06 23:55 -0500 (Sat, 06 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4879
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4668
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 6/31HostnameOS / ArchCHECK
biodbHmdb 1.16.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-12-06 09:55 -0500 (Sat, 06 Dec 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_22
git_last_commit: 4102973
git_last_commit_date: 2025-10-29 11:13:48 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on merida1

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

raw results


Summary

Package: biodbHmdb
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
StartedAt: 2025-12-06 16:01:29 -0500 (Sat, 06 Dec 2025)
EndedAt: 2025-12-06 16:03:04 -0500 (Sat, 06 Dec 2025)
EllapsedTime: 94.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-12-06 16:02:59.994][biodb::testContext]
biodb.INFO [2025-12-06 16:02:59.998][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-06 16:03:00.000][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-12-06 16:03:00.001][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-06 16:03:00.002][biodb::testContext]
biodb.INFO [2025-12-06 16:03:00.009][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-06 16:03:00.012][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-12-06 16:03:00.019][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:03:00.021][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-06 16:03:00.023][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-06 16:03:00.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.028][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-06 16:03:00.053][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-06 16:03:00.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.058][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-06 16:03:00.060][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-06 16:03:00.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.074][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-06 16:03:00.075][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-06 16:03:00.077][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-06 16:03:00.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.081][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-06 16:03:00.083][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-06 16:03:00.084][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-06 16:03:00.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.088][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-06 16:03:00.090][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-06 16:03:00.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.093][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".
biodb.DEBUG[2025-12-06 16:03:00.094][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-06 16:03:00.095][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-06 16:03:00.097][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-06 16:03:00.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.101][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-06 16:03:00.102][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-06 16:03:00.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.107][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-06 16:03:00.108][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-06 16:03:00.109][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-06 16:03:00.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.114][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-06 16:03:00.115][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-06 16:03:00.116][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-06 16:03:00.118][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-06 16:03:00.119][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-06 16:03:00.120][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-06 16:03:00.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.125][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-06 16:03:00.126][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-06 16:03:00.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.131][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-06 16:03:00.132][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-06 16:03:00.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.135][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[2025-12-06 16:03:00.136][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-06 16:03:00.138][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-06 16:03:00.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.142][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-06 16:03:00.144][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-06 16:03:00.145][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-06 16:03:00.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.149][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-06 16:03:00.151][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-06 16:03:00.161][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-06 16:03:00.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.166][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-06 16:03:00.167][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-06 16:03:00.168][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-06 16:03:00.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.175][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-06 16:03:00.217][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:00.238][self$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[2025-12-06 16:03:00.240][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.242][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:03:00.245][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.246][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:03:00.248][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:00.249][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:03:00.250][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-06 16:03:00.251][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:03:00.253][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.254][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-06 16:03:00.256][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:03:00.258][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:00.259][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.260][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:03:00.260][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:03:00.260][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:03:00.260][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-06 16:03:00.260][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-06 16:03:00.261][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:03:00.263][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:00.264][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:00.265][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:03:00.266][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:00.267][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:00.269][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:03:00.270][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:00.271][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:03:00.272][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:03:00.273][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:00.275][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:00.276][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-06 16:03:00.278][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:00.280][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-06 16:03:00.281][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.282][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:03:00.283][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.285][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:03:00.286][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:00.287][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:03:00.288][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-06 16:03:00.290][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:03:00.296][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.297][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-06 16:03:00.298][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:03:00.299][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:00.300][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.302][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:03:00.302][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:03:00.302][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:03:00.302][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-06 16:03:00.302][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-06 16:03:00.303][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:03:00.304][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:00.305][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:00.306][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:03:00.308][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:00.309][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:00.310][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:03:00.311][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:00.312][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:03:00.313][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:03:00.314][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:00.316][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:00.317][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-06 16:03:00.321][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.322][self$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[2025-12-06 16:03:00.324][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.325][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:03:00.326][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.327][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:03:00.329][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:00.330][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:03:00.331][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-06 16:03:00.332][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:03:00.333][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:00.335][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-06 16:03:00.336][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:03:00.337][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:00.338][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.339][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:00.341][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:03:00.342][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:00.343][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:00.344][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:03:00.345][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:00.346][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:00.348][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:03:00.349][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:00.350][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:03:00.351][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:03:00.352][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:00.353][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:00.355][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-06 16:03:00.357][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.358][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-06 16:03:00.360][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.361][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:03:00.362][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.363][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:03:00.364][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:00.366][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:03:00.367][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-06 16:03:00.368][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:03:00.369][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:00.371][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-06 16:03:00.372][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:03:00.373][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:00.374][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.376][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:00.377][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:03:00.378][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:00.379][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:00.380][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:03:00.381][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:00.383][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:00.384][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:03:00.385][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:00.386][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:03:00.387][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:03:00.388][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:00.390][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:00.394][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:03:00.395][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.486][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-06 16:03:00.491][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-06 16:03:00.493][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-06 16:03:00.495][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-06 16:03:00.496][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-06 16:03:00.498][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-06 16:03:00.500][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-06 16:03:00.505][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-06 16:03:00.507][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-06 16:03:00.509][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-06 16:03:00.511][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-06 16:03:00.512][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-06 16:03:00.514][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-06 16:03:00.516][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-06 16:03:00.517][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-06 16:03:00.519][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-06 16:03:00.521][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-06 16:03:00.522][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-06 16:03:00.524][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-06 16:03:00.526][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-06 16:03:00.527][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-06 16:03:00.529][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-06 16:03:00.531][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-06 16:03:00.533][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-06 16:03:00.534][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-06 16:03:00.536][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-06 16:03:00.538][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-06 16:03:00.539][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-06 16:03:00.541][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-06 16:03:00.543][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-06 16:03:00.544][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-06 16:03:00.546][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-06 16:03:00.548][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-06 16:03:00.549][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-06 16:03:00.551][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-06 16:03:00.553][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-06 16:03:00.554][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-06 16:03:00.556][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-06 16:03:00.558][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-06 16:03:00.559][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-06 16:03:00.561][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-06 16:03:00.563][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-06 16:03:00.564][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-06 16:03:00.566][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-06 16:03:00.568][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-06 16:03:00.569][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-06 16:03:00.571][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-06 16:03:00.573][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-06 16:03:00.575][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-06 16:03:00.576][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-06 16:03:00.578][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-06 16:03:00.580][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-06 16:03:00.581][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-06 16:03:00.583][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-06 16:03:00.585][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-06 16:03:00.586][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-06 16:03:00.588][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-06 16:03:00.590][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-06 16:03:00.591][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-06 16:03:00.593][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-06 16:03:00.595][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-06 16:03:00.596][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-06 16:03:00.598][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-06 16:03:00.600][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-06 16:03:00.601][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-06 16:03:00.603][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-06 16:03:00.605][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-06 16:03:00.606][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-06 16:03:00.608][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-06 16:03:00.610][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-06 16:03:00.611][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-06 16:03:00.613][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-06 16:03:00.615][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-06 16:03:00.616][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-06 16:03:00.618][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-06 16:03:00.620][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-06 16:03:00.621][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-06 16:03:00.623][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-06 16:03:00.625][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-06 16:03:00.626][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-06 16:03:00.628][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-06 16:03:00.630][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-06 16:03:00.631][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-06 16:03:00.639][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-06 16:03:00.641][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-06 16:03:00.644][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:03:00.645][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.647][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:00.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:00.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:00.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:00.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:00.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:00.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:00.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:00.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:00.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:00.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:00.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:00.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:00.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:00.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:00.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:00.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:00.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:00.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:00.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:00.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:00.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:00.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:00.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:00.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:00.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:00.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:00.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:00.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:00.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:00.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:00.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:00.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.781][FUN] Functions in observer BiodbConfig: [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 [2025-12-06 16:03:00.783][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-12-06 16:03:00.792][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-12-06 16:03:00.811][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-12-06 16:03:00.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:00.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:00.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:00.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:00.821][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-12-06 16:03:00.834][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-12-06 16:03:00.836][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:00.838][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-12-06 16:03:00.839][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.840][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:03:00.841][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:00.843][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-12-06 16:03:00.844][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.845][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:03:00.846][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-06 16:03:00.848][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:03:00.849][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.850][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-12-06 16:03:00.851][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:03:00.853][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-12-06 16:03:00.853][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-12-06 16:03:00.853][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-12-06 16:03:00.853][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-12-06 16:03:00.853][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-12-06 16:03:00.853][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-12-06 16:03:00.853][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-12-06 16:03:00.853][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-12-06 16:03:00.853][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-12-06 16:03:00.853][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-12-06 16:03:00.853][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-12-06 16:03:00.853][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-12-06 16:03:00.853][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-12-06 16:03:00.853][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-12-06 16:03:00.853][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-12-06 16:03:00.853][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-12-06 16:03:00.853][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-12-06 16:03:00.853][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-12-06 16:03:00.854][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:00.855][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:03:00.855][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-12-06 16:03:00.855][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-12-06 16:03:00.857][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-06 16:03:00.858][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:00.859][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:00.860][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:03:00.861][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:00.863][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:00.864][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:03:00.865][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-12-06 16:03:00.865][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-12-06 16:03:00.866][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:03:00.867][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:03:00.868][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:00.870][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:00.877][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-12-06 16:03:00.879][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-06 16:03:00.881][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-06 16:03:00.884][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-06 16:03:00.886][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-06 16:03:00.913][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-12-06 16:03:00.928][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-12-06 16:03:00.937][biodb::testThat]
biodb.INFO [2025-12-06 16:03:00.938][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-06 16:03:00.940][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:03:00.941][biodb::testThat]
biodb.TRACE[2025-12-06 16:03:00.945][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-12-06 16:03:00.947][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-12-06 16:03:00.950][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-12-06 16:03:00.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-06 16:03:00.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:00.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:00.976][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:00.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:00.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:00.980][FUN] Functions in observer BiodbConfig: [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[2025-12-06 16:03:00.991][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:00.993][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:00.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:00.995][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:00.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.018][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.020][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.022][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.057][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.063][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:03:01.064][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:03:01.065][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.066][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.068][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:03:01.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:03:01.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.073][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:01.074][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:01.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.077][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.078][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:01.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:01.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.083][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.085][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.087][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.094][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.095][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.097][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.112][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:01.114][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:01.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.116][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.118][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:01.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:01.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.123][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.124][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.126][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.128][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.133][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:01.134][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:01.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.136][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.138][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:01.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:01.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.143][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:01.144][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:01.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.146][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.148][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:01.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:01.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.153][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:01.154][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:01.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.157][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.158][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:01.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:01.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.163][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:01.164][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:01.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.167][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.168][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:01.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:01.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.173][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:01.174][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:01.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.177][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.178][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:01.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:01.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.183][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:01.184][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:01.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.187][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:01.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:01.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.193][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:01.195][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:01.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.197][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.198][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:01.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:01.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.203][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:03:01.205][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:03:01.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.207][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.208][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:03:01.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:03:01.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.213][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:03:01.215][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:03:01.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.217][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.219][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:03:01.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:03:01.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.224][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-12-06 16:03:01.225][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:01.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.227][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.229][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-12-06 16:03:01.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:01.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.329][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:03:01.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:03:01.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.334][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:03:01.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:03:01.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.339][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:03:01.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:03:01.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.344][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:01.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:01.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.348][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:01.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:01.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.353][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:01.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:01.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.388][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:01.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:01.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.392][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:01.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:01.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.397][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:01.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:01.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.402][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:01.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:01.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.407][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:01.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:01.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.412][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:01.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:01.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.417][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:01.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:01.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.422][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:01.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:01.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.427][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:01.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:01.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.432][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:03:01.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:03:01.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.436][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:03:01.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:03:01.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.441][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:03:01.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:03:01.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.446][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:01.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:01.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.451][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:01.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:01.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.459][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:01.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:01.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.464][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:01.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:01.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.469][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:01.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:01.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.474][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:01.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:01.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.479][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:01.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:01.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:01.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:01.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.488][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:01.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:01.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.493][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:01.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:01.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.498][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:01.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:01.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.503][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:01.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:01.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:01.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:01.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:01.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:01.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:01.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:01.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.523][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:01.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:01.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.527][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:01.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:01.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.532][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:01.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:01.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.537][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.542][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.547][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.552][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.557][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.561][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.566][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:03:01.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:03:01.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.571][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:03:01.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:03:01.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.576][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:03:01.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:03:01.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.581][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-12-06 16:03:01.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:01.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:01.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:01.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.591][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:01.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:01.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:01.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:01.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.600][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-12-06 16:03:01.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:01.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.632][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:01.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:01.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.637][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:01.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:01.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:01.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:01.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.647][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:01.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:01.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.652][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:01.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:01.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.657][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:03:01.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:03:01.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.662][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:03:01.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:03:01.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.671][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:03:01.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:03:01.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-06 16:03:01.705][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-12-06 16:03:01.708][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-06 16:03:01.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-06 16:03:01.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.713][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-06 16:03:01.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-06 16:03:01.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.718][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-06 16:03:01.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-06 16:03:01.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.723][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-06 16:03:01.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-06 16:03:01.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.740][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:03:01.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:03:01.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.785][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:03:01.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:03:01.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.790][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:03:01.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:03:01.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.795][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:03:01.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:03:01.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.823][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.825][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.827][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:01.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:01.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.843][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.849][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.853][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.858][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.860][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.862][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.863][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:01.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.893][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.895][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.897][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:01.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.914][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.919][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.924][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.929][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.930][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.932][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.934][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:01.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.963][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.968][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.969][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.971][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:03:01.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.987][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:01.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:01.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.993][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:01.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:01.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:01.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:01.997][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:01.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:02.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.002][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:02.004][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:02.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.006][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.007][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:02.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:02.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.023][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:02.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:02.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.028][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:02.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:02.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.033][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:02.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:02.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.038][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:02.039][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:02.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.041][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.043][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:02.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:02.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.058][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:03:02.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:03:02.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.063][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:03:02.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:03:02.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.068][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:03:02.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:03:02.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.073][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:03:02.074][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:03:02.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.077][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.078][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:03:02.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:03:02.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.093][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:02.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:02.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.098][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:02.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:02.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.107][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:02.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:02.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.112][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:02.113][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:02.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.116][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.117][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:02.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:02.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.132][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:03:02.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:03:02.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.137][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:03:02.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:03:02.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.142][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:03:02.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:03:02.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.147][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:03:02.149][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:03:02.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.151][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.152][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:03:02.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:03:02.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:02.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:02.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:02.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:02.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:02.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:02.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.182][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:02.184][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:02.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.186][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:02.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:02.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.202][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:02.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:02.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.207][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:02.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:02.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.212][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:02.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:02.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.217][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:02.219][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:02.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.221][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.222][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:02.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:02.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.239][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:02.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:02.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.244][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:02.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:02.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.249][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:02.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:02.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.254][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:02.255][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:02.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.258][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.259][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:02.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:02.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.279][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:02.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:02.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.284][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:02.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:02.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.289][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:02.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:02.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.294][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:02.295][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:02.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.298][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.299][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:02.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:02.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.314][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:03:02.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:03:02.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.319][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:03:02.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:03:02.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.324][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:03:02.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:03:02.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.329][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:03:02.331][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:03:02.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.333][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.334][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:03:02.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:03:02.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:02.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:02.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:02.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:02.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.359][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:02.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:02.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.364][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:02.365][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:02.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.368][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.369][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:02.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:02.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.384][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:02.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:02.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.389][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:02.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:02.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:02.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:02.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.399][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:02.400][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:02.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.402][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.404][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:02.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:02.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.419][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:02.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:02.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.424][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:02.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:02.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.429][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:02.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:02.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.438][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:02.440][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:02.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.442][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.444][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:02.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:02.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.460][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:02.461][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:02.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.464][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.470][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:03:02.471][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:03:02.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.474][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.480][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:02.481][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:02.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.484][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.490][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:03:02.491][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:03:02.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.494][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.500][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:02.501][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:03:02.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.504][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.510][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:02.512][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:03:02.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.514][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.520][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:02.522][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:03:02.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.524][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.531][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:02.532][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:03:02.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.535][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.541][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:03:02.542][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:03:02.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.545][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.551][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:02.553][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:02.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.555][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.562][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:02.563][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:02.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.566][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.572][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:02.574][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:02.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.576][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.583][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:02.584][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:03:02.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.586][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.593][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:02.594][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:03:02.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.597][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.603][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:02.605][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:02.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.607][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.613][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:02.619][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:03:02.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.621][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.628][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:02.629][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:02.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.631][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:02.638][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:03:02.639][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:03:02.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.642][ef$get] fields variable is a list.
biodb.INFO [2025-12-06 16:03:02.652][biodb::testThat]
biodb.INFO [2025-12-06 16:03:02.653][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-06 16:03:02.654][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:03:02.655][biodb::testThat]
biodb.DEBUG[2025-12-06 16:03:02.674][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-06 16:03:02.677][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-06 16:03:02.680][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-06 16:03:02.719][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-06 16:03:02.721][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-06 16:03:02.722][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-06 16:03:02.896][biodb::testThat]
biodb.INFO [2025-12-06 16:03:02.898][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-06 16:03:02.899][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:03:02.900][biodb::testThat]
biodb.TRACE[2025-12-06 16:03:02.904][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:02.905][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:02.907][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:02.913][ef$get] fields variable is a list.
biodb.DEBUG[2025-12-06 16:03:02.915][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-12-06 16:03:02.944][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-06 16:03:03.007][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-06 16:03:03.009][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-06 16:03:03.010][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-06 16:03:03.012][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-06 16:03:03.029][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-06 16:03:03.105][biodb::testThat]
biodb.INFO [2025-12-06 16:03:03.106][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-06 16:03:03.107][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:03:03.108][biodb::testThat]
biodb.DEBUG[2025-12-06 16:03:03.119][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-06 16:03:03.120][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-06 16:03:03.122][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-06 16:03:03.124][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-06 16:03:03.125][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-06 16:03:03.127][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-06 16:03:03.187][biodb::testThat]
biodb.INFO [2025-12-06 16:03:03.189][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-06 16:03:03.190][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:03:03.191][biodb::testThat]
biodb.DEBUG[2025-12-06 16:03:03.196][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-06 16:03:03.197][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-06 16:03:03.199][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-06 16:03:03.200][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-06 16:03:03.202][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-06 16:03:03.203][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-06 16:03:03.258][biodb::testThat]
biodb.INFO [2025-12-06 16:03:03.260][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-06 16:03:03.261][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:03:03.262][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-06 16:03:03.322][biodb::testThat]
biodb.INFO [2025-12-06 16:03:03.324][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-06 16:03:03.325][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:03:03.326][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-06 16:03:03.383][biodb::testThat]
biodb.INFO [2025-12-06 16:03:03.385][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-06 16:03:03.386][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:03:03.387][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-06 16:03:03.449][biodb::testThat]
biodb.INFO [2025-12-06 16:03:03.450][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-06 16:03:03.451][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:03:03.452][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2025-12-06 16:03:03.527][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:03.529][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:03.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:03.531][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:03.533][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:03:03.534][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:03:03.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:03.536][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:03.537][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:03.539][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:03.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:03.541][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:03.543][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:03.544][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:03.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:03.546][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:03.548][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:03:03.549][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:03:03.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:03.551][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:03.552][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:03.554][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:03:03.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:03.556][ef$get] fields variable is a list.
biodb.INFO [2025-12-06 16:03:03.557][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-06 16:03:03.559][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-12-06 16:03:03.560][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-06 16:03:03.561][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:03.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:03.563][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:03.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:03.570][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:03.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]

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

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

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

'R CMD check' output

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


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

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

Installation output

biodbHmdb.Rcheck/00install.out

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