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 nebbiolo2

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

raw results


Summary

Package: biodbHmdb
Version: 1.16.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
StartedAt: 2025-12-06 16:01:08 -0500 (Sat, 06 Dec 2025)
EndedAt: 2025-12-06 16:02:17 -0500 (Sat, 06 Dec 2025)
EllapsedTime: 69.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
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 16:02:14.102][biodb::testContext]
biodb.INFO [2025-12-06 16:02:14.104][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-06 16:02:14.105][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-12-06 16:02:14.106][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-06 16:02:14.107][biodb::testContext]
biodb.INFO [2025-12-06 16:02:14.113][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-06 16:02:14.114][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-12-06 16:02:14.121][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:02:14.122][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-06 16:02:14.123][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-06 16:02:14.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:14.127][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-06 16:02:14.143][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-06 16:02:14.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.147][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-06 16:02:14.148][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-06 16:02:14.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:14.160][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-06 16:02:14.161][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-06 16:02:14.161][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-06 16:02:14.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.164][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 16:02:14.165][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-06 16:02:14.166][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-06 16:02:14.167][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-06 16:02:14.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:14.170][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-06 16:02:14.171][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-06 16:02:14.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.175][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-06 16:02:14.175][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-06 16:02:14.176][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-06 16:02:14.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:14.180][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-06 16:02:14.181][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-06 16:02:14.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.184][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-06 16:02:14.185][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-06 16:02:14.186][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-06 16:02:14.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:14.189][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-06 16:02:14.190][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-06 16:02:14.191][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-06 16:02:14.192][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-06 16:02:14.193][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-06 16:02:14.194][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-06 16:02:14.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.197][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-06 16:02:14.198][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-06 16:02:14.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:14.202][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-06 16:02:14.203][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-06 16:02:14.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.206][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-06 16:02:14.207][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-06 16:02:14.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:14.210][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-06 16:02:14.211][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-06 16:02:14.212][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-06 16:02:14.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.215][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-06 16:02:14.216][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-06 16:02:14.220][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-06 16:02:14.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:14.224][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-06 16:02:14.225][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-06 16:02:14.225][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-06 16:02:14.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.231][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-06 16:02:14.261][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:14.276][self$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 16:02:14.277][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.278][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:14.278][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.279][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:14.280][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:14.281][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:14.282][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-06 16:02:14.283][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:14.284][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.285][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-06 16:02:14.286][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:14.287][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:14.288][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.289][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:14.289][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:02:14.289][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:02:14.289][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-06 16:02:14.289][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-06 16:02:14.290][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:14.291][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:14.291][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:14.292][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:14.293][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:14.294][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:14.295][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:14.296][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:14.297][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:14.297][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:14.298][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:14.299][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:14.300][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-06 16:02:14.302][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:14.303][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-06 16:02:14.304][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.305][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:14.306][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.307][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:14.308][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:14.313][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:14.314][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-06 16:02:14.315][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:14.316][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.316][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-06 16:02:14.317][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:14.318][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:14.319][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.320][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:14.320][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:02:14.320][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:02:14.320][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-06 16:02:14.320][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-06 16:02:14.321][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:14.322][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:14.323][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:14.324][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:14.325][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:14.325][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:14.326][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:14.327][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:14.328][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:14.329][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:14.330][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:14.331][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:14.332][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-06 16:02:14.334][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.334][self$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 16:02:14.335][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.336][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:14.337][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.338][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:14.339][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:14.340][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:14.341][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-06 16:02:14.342][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:14.343][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:14.344][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-06 16:02:14.345][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:14.346][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:14.346][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.347][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:14.348][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:14.349][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:14.350][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:14.351][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:14.352][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:14.353][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:14.353][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:14.354][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:14.355][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:14.356][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:14.357][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:14.358][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:14.359][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-06 16:02:14.360][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.361][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-06 16:02:14.362][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.363][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:14.364][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.365][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:14.366][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:14.367][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:14.368][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-06 16:02:14.369][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:14.370][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:14.371][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-06 16:02:14.372][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:14.372][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:14.373][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.374][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:14.375][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:14.376][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:14.377][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:14.378][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:14.379][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:14.380][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:14.380][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:14.381][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:14.382][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:14.383][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:14.384][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:14.385][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:14.388][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:02:14.389][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.392][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 16:02:14.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.397][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 16:02:14.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.401][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 16:02:14.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.402][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 16:02:14.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.405][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 16:02:14.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.409][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 16:02:14.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.413][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 16:02:14.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.417][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 16:02:14.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:14.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.421][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 16:02:14.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:14.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.425][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 16:02:14.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:14.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.429][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 16:02:14.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:14.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.434][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 16:02:14.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.435][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 16:02:14.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.438][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 16:02:14.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.442][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 16:02:14.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.446][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 16:02:14.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.450][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 16:02:14.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.452][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 16:02:14.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.454][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 16:02:14.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.457][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-06 16:02:14.469][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-06 16:02:14.472][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-06 16:02:14.474][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-06 16:02:14.475][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-06 16:02:14.495][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-06 16:02:14.497][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-06 16:02:14.498][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-06 16:02:14.500][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-06 16:02:14.501][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-06 16:02:14.503][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-06 16:02:14.504][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-06 16:02:14.506][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-06 16:02:14.507][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-06 16:02:14.509][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-06 16:02:14.510][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-06 16:02:14.512][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-06 16:02:14.513][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-06 16:02:14.515][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-06 16:02:14.517][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-06 16:02:14.518][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-06 16:02:14.519][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-06 16:02:14.521][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-06 16:02:14.522][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-06 16:02:14.524][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-06 16:02:14.525][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-06 16:02:14.527][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-06 16:02:14.528][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-06 16:02:14.529][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-06 16:02:14.531][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-06 16:02:14.532][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-06 16:02:14.534][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-06 16:02:14.535][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-06 16:02:14.536][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-06 16:02:14.538][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-06 16:02:14.539][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-06 16:02:14.541][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-06 16:02:14.542][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-06 16:02:14.544][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-06 16:02:14.545][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-06 16:02:14.546][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-06 16:02:14.548][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-06 16:02:14.549][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-06 16:02:14.551][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-06 16:02:14.552][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-06 16:02:14.553][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-06 16:02:14.555][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-06 16:02:14.556][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-06 16:02:14.558][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-06 16:02:14.559][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-06 16:02:14.561][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-06 16:02:14.562][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-06 16:02:14.563][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-06 16:02:14.565][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-06 16:02:14.566][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-06 16:02:14.567][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-06 16:02:14.569][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-06 16:02:14.570][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-06 16:02:14.572][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-06 16:02:14.573][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-06 16:02:14.574][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-06 16:02:14.576][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-06 16:02:14.577][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-06 16:02:14.579][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-06 16:02:14.580][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-06 16:02:14.581][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-06 16:02:14.583][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-06 16:02:14.584][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-06 16:02:14.586][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-06 16:02:14.587][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-06 16:02:14.588][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-06 16:02:14.590][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-06 16:02:14.591][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-06 16:02:14.593][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-06 16:02:14.594][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-06 16:02:14.595][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-06 16:02:14.597][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-06 16:02:14.598][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-06 16:02:14.600][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-06 16:02:14.601][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-06 16:02:14.602][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-06 16:02:14.604][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-06 16:02:14.605][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-06 16:02:14.612][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-06 16:02:14.613][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-06 16:02:14.617][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:02:14.617][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.618][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 16:02:14.619][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:14.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:14.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:14.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:14.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:14.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:14.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.635][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 16:02:14.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:14.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:14.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:14.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:14.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:14.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:14.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.647][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 16:02:14.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:14.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:14.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:14.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:14.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:14.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.663][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 16:02:14.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:14.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:14.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:14.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:14.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:14.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:14.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.675][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 16:02:14.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.676][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 16:02:14.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:14.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:14.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.680][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 16:02:14.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:14.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:14.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:14.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.686][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 16:02:14.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:14.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:14.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:14.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.692][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 16:02:14.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:14.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:14.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.698][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 16:02:14.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:14.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:14.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.703][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 16:02:14.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:14.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:14.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.709][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 16:02:14.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:14.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:14.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.715][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 16:02:14.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:14.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:14.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:14.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.721][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 16:02:14.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.722][FUN] Functions in observer BiodbConfig: [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 16:02:14.723][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-12-06 16:02:14.732][private$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 16:02:14.744][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-12-06 16:02:14.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:14.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:14.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:14.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.748][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 16:02:14.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.752][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-12-06 16:02:14.760][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-12-06 16:02:14.762][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:14.763][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-12-06 16:02:14.764][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.765][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:14.766][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:14.767][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-12-06 16:02:14.768][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.769][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:14.769][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-06 16:02:14.770][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:14.771][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.772][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-12-06 16:02:14.773][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:14.774][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-12-06 16:02:14.774][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-12-06 16:02:14.774][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-12-06 16:02:14.774][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-12-06 16:02:14.774][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-12-06 16:02:14.774][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-12-06 16:02:14.774][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-12-06 16:02:14.774][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-12-06 16:02:14.774][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-12-06 16:02:14.774][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-12-06 16:02:14.774][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-12-06 16:02:14.774][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-12-06 16:02:14.774][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-12-06 16:02:14.774][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-12-06 16:02:14.774][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-12-06 16:02:14.774][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-12-06 16:02:14.774][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-12-06 16:02:14.774][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-12-06 16:02:14.775][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:14.776][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:14.776][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-12-06 16:02:14.776][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-12-06 16:02:14.777][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-06 16:02:14.778][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:14.779][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:14.780][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:14.780][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:14.781][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:14.782][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:14.783][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-12-06 16:02:14.783][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-12-06 16:02:14.784][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:14.785][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:14.786][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:14.787][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:14.792][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-12-06 16:02:14.793][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-06 16:02:14.795][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-06 16:02:14.796][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-06 16:02:14.798][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-06 16:02:14.821][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-12-06 16:02:14.835][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-12-06 16:02:14.843][biodb::testThat]
biodb.INFO [2025-12-06 16:02:14.844][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-06 16:02:14.845][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:14.845][biodb::testThat]
biodb.TRACE[2025-12-06 16:02:14.849][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-12-06 16:02:14.850][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-12-06 16:02:14.854][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-12-06 16:02:14.861][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-06 16:02:14.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:14.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:14.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:14.875][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 16:02:14.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:14.877][FUN] Functions in observer BiodbConfig: [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 16:02:14.887][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:14.888][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:14.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:14.890][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:14.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:14.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:14.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:14.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:14.907][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:14.908][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:14.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:14.909][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:14.933][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:14.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:14.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:14.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:14.937][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:02:14.938][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:02:14.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:14.940][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:14.941][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:02:14.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:02:14.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:14.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:14.945][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:02:14.946][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:02:14.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:14.948][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:14.949][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:02:14.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:02:14.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:14.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:14.953][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:02:14.954][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:02:14.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:14.955][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:14.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:02:14.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:02:14.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:14.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:14.961][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:14.961][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:14.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:14.963][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:14.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:14.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:14.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:14.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:14.977][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:14.978][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:14.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:14.979][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:14.980][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:14.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:14.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:14.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:14.984][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:14.985][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:14.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:14.987][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:14.988][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:14.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:14.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:14.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:14.992][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:14.993][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:14.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:14.995][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:14.996][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:14.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:14.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:14.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.000][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.001][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.002][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.003][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.007][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:15.008][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:15.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.010][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.011][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:15.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:15.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.015][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:15.016][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:15.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.017][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:15.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:15.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.022][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.023][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.025][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.026][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.030][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.031][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.033][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.038][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:15.039][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:15.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.040][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.041][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:15.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:15.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.045][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:02:15.046][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:02:15.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.048][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.049][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:02:15.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:02:15.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.053][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:02:15.054][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:02:15.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.055][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.057][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:02:15.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:02:15.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.060][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-12-06 16:02:15.061][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:15.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.063][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.064][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-12-06 16:02:15.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:15.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.149][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:02:15.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:02:15.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.153][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:02:15.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:02:15.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.157][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:02:15.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:02:15.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.160][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:02:15.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:02:15.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.164][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:02:15.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:02:15.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.168][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:02:15.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:02:15.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:02:15.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:02:15.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:02:15.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:02:15.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:02:15.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:02:15.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:15.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:15.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:15.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:15.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:15.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:15.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.193][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:15.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:15.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.197][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:15.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:15.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.201][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:15.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:15.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.204][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.208][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.212][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.215][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:15.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:15.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.219][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:15.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:15.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.223][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:15.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:15.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.226][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:02:15.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:02:15.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.230][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:02:15.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:02:15.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.234][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:02:15.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:02:15.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.237][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:15.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:15.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.241][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:15.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:15.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.248][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:15.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:15.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.252][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:15.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:15.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.255][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:15.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:15.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.259][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:15.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:15.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.266][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.274][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:15.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:15.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.277][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:15.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:15.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.281][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:15.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:15.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.296][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:15.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:15.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.299][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:15.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:15.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.303][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:15.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:15.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.307][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:15.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:15.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.310][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:15.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:15.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.314][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:15.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:15.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.318][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:15.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:15.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.321][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:15.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:15.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.325][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:15.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:15.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.329][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:02:15.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:02:15.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.332][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:02:15.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:02:15.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.336][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:02:15.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:02:15.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.340][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-12-06 16:02:15.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.343][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.347][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.351][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.354][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-12-06 16:02:15.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.378][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:15.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:15.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.381][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:15.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:15.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.385][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:15.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:15.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.389][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:15.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:15.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.392][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:15.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:15.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.396][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:02:15.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:02:15.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.400][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:02:15.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:02:15.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.407][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:02:15.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:02:15.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-06 16:02:15.433][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-12-06 16:02:15.435][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-06 16:02:15.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-06 16:02:15.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.439][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-06 16:02:15.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-06 16:02:15.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.442][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-06 16:02:15.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-06 16:02:15.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.446][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-06 16:02:15.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-06 16:02:15.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.458][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:02:15.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:02:15.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.493][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:02:15.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:02:15.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.496][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:02:15.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:02:15.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.500][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:02:15.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-06 16:02:15.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.520][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.521][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.523][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.535][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:15.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:15.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.538][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:15.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:15.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.542][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:15.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:15.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.546][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:15.547][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:15.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.548][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.549][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:15.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:15.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:15.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:15.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:15.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:15.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:15.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:15.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.571][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:15.572][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:15.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.574][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:15.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:15.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.585][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:15.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:15.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.589][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:15.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:15.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.592][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:15.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:15.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.596][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:15.597][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:15.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.599][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.600][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:15.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:15.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:02:15.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:02:15.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:02:15.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:02:15.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:02:15.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:02:15.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.625][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:02:15.626][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:02:15.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.628][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:02:15.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:02:15.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.640][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:15.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:15.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.643][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:15.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:15.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.647][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:15.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:15.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.651][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:15.652][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:15.653][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.653][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.654][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:15.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:15.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.665][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:15.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:15.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.668][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:15.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:15.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:15.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:15.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.676][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:15.677][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:15.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.679][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.680][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:15.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:15.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.690][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:02:15.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:02:15.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.694][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:02:15.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:02:15.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.697][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:02:15.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:02:15.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.701][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:02:15.702][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:02:15.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.704][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.705][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:02:15.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:02:15.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.715][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:15.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:15.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.719][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:15.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:15.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.726][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:15.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:15.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.730][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:15.731][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:15.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.732][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.733][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:15.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:15.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.744][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:02:15.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:02:15.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.748][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:02:15.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:02:15.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.751][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:02:15.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:02:15.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.755][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:02:15.756][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:02:15.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.758][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.759][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:02:15.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:02:15.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.780][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.781][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.783][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:15.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.794][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:15.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:15.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.798][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:15.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:15.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.802][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:15.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:15.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.805][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:15.806][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:15.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.808][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.809][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:15.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:15.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.819][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:15.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:15.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.823][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:15.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:15.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.827][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:15.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:15.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.830][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:15.831][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:15.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.833][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.834][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:15.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:15.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.848][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.852][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.856][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.859][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.860][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.862][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.863][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:15.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.873][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:02:15.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:02:15.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.877][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:02:15.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:02:15.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.881][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:02:15.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:02:15.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.884][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:02:15.885][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:02:15.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.887][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.888][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:02:15.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:02:15.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.898][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:15.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:15.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.902][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:15.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:15.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.906][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:15.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:15.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.909][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:15.910][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:15.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.912][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:15.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:15.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.923][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.927][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.931][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.935][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.935][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.937][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.938][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:15.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.948][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:02:15.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:02:15.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.952][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:02:15.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:02:15.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.956][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:02:15.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:02:15.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.964][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:02:15.965][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:02:15.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.967][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.968][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:02:15.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:02:15.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.979][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:15.980][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:15.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.981][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.985][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-06 16:02:15.986][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-06 16:02:15.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.988][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.992][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:02:15.993][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:02:15.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:15.995][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:15.999][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-06 16:02:16.000][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-06 16:02:16.000][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.001][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.005][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:16.006][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-06 16:02:16.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.008][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.012][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:16.013][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:16.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.015][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.019][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:16.020][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:16.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.021][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.025][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:16.026][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-06 16:02:16.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.028][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.032][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:02:16.033][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:02:16.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.035][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.038][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:16.039][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:16.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.041][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.045][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:16.046][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:16.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.048][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.052][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:16.053][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:16.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.054][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.058][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:16.059][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-06 16:02:16.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.061][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.065][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:16.066][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:16.067][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.067][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.071][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:16.072][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:16.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.074][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.082][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:16.083][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:16.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.084][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.088][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:16.089][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:16.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.091][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.095][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-12-06 16:02:16.096][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-06 16:02:16.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.098][ef$get] fields variable is a list.
biodb.INFO [2025-12-06 16:02:16.104][biodb::testThat]
biodb.INFO [2025-12-06 16:02:16.105][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-06 16:02:16.106][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:16.106][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:16.119][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-06 16:02:16.121][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-06 16:02:16.124][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-06 16:02:16.151][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-06 16:02:16.152][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-06 16:02:16.153][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-06 16:02:16.278][biodb::testThat]
biodb.INFO [2025-12-06 16:02:16.279][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-06 16:02:16.280][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:16.280][biodb::testThat]
biodb.TRACE[2025-12-06 16:02:16.283][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:16.290][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:16.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.291][ef$get] fields variable is a list.
biodb.DEBUG[2025-12-06 16:02:16.292][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-12-06 16:02:16.312][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-06 16:02:16.355][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-06 16:02:16.356][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-06 16:02:16.357][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-06 16:02:16.358][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-06 16:02:16.370][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-06 16:02:16.425][biodb::testThat]
biodb.INFO [2025-12-06 16:02:16.426][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-06 16:02:16.427][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:16.428][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:16.434][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-06 16:02:16.435][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-06 16:02:16.437][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-06 16:02:16.438][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-06 16:02:16.439][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-06 16:02:16.440][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-06 16:02:16.484][biodb::testThat]
biodb.INFO [2025-12-06 16:02:16.485][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-06 16:02:16.486][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:16.487][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:16.491][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-06 16:02:16.492][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-06 16:02:16.493][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-06 16:02:16.494][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-06 16:02:16.495][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-06 16:02:16.496][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-06 16:02:16.536][biodb::testThat]
biodb.INFO [2025-12-06 16:02:16.537][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-06 16:02:16.538][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:16.539][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-06 16:02:16.583][biodb::testThat]
biodb.INFO [2025-12-06 16:02:16.584][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-06 16:02:16.585][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:16.586][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-06 16:02:16.626][biodb::testThat]
biodb.INFO [2025-12-06 16:02:16.627][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-06 16:02:16.628][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:16.629][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-06 16:02:16.673][biodb::testThat]
biodb.INFO [2025-12-06 16:02:16.674][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-06 16:02:16.675][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:16.676][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2025-12-06 16:02:16.729][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:16.730][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:16.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.732][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.733][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:02:16.734][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:02:16.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.736][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.736][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:16.737][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:16.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.739][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.740][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:16.741][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:16.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.743][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.744][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:02:16.745][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:02:16.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.747][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:16.748][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:16.748][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-06 16:02:16.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:16.750][ef$get] fields variable is a list.
biodb.INFO [2025-12-06 16:02:16.751][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-06 16:02:16.752][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-12-06 16:02:16.753][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-06 16:02:16.758][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:16.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:16.759][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:16.760][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 16:02:16.761][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:16.762][FUN] Functions in observer 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:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.16.0’
* 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 ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking 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, 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log’
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.16.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor ‘EntryMaker::EntryMaker()’:
EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
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)