Back to Long Tests report for BioC 3.22

This page was generated on 2026-04-04 23:55 -0400 (Sat, 04 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4897
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4691
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: 2026-04-04 09:55 -0400 (Sat, 04 Apr 2026)
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 -0400 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on merida1

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

raw results


Summary

Package: biodbHmdb
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
StartedAt: 2026-04-04 16:01:13 -0400 (Sat, 04 Apr 2026)
EndedAt: 2026-04-04 16:02:43 -0400 (Sat, 04 Apr 2026)
EllapsedTime: 89.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
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 [2026-04-04 16:02:38.140][biodb::testContext]
biodb.INFO [2026-04-04 16:02:38.144][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:02:38.145][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-04-04 16:02:38.146][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:02:38.147][biodb::testContext]
biodb.INFO [2026-04-04 16:02:38.154][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:02:38.156][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-04-04 16:02:38.163][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:38.164][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-04-04 16:02:38.166][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-04-04 16:02:38.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:38.171][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-04-04 16:02:38.195][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-04-04 16:02:38.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.198][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.200][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-04-04 16:02:38.201][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-04-04 16:02:38.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:38.206][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-04-04 16:02:38.207][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-04-04 16:02:38.208][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-04-04 16:02:38.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.212][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.213][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-04-04 16:02:38.214][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-04-04 16:02:38.216][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-04-04 16:02:38.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:38.220][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-04-04 16:02:38.221][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-04-04 16:02:38.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.225][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.226][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-04-04 16:02:38.227][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-04-04 16:02:38.229][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-04-04 16:02:38.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:38.233][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-04-04 16:02:38.235][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-04-04 16:02:38.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.238][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.239][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-04-04 16:02:38.240][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-04-04 16:02:38.242][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-04-04 16:02:38.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:38.246][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:02:38.248][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-04-04 16:02:38.249][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-04-04 16:02:38.250][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-04-04 16:02:38.251][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-04-04 16:02:38.253][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-04-04 16:02:38.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.256][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.257][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-04-04 16:02:38.259][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-04-04 16:02:38.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:38.263][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-04-04 16:02:38.265][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-04-04 16:02:38.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.268][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.269][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-04-04 16:02:38.271][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-04-04 16:02:38.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:38.275][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-04-04 16:02:38.276][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-04-04 16:02:38.278][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-04-04 16:02:38.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.281][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.283][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:02:38.284][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-04-04 16:02:38.295][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-04-04 16:02:38.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:38.300][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-04-04 16:02:38.301][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-04-04 16:02:38.302][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-04-04 16:02:38.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.306][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.309][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-04-04 16:02:38.353][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:38.383][self$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[2026-04-04 16:02:38.384][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:38.385][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:38.387][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:38.388][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:38.389][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:38.391][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:38.392][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:02:38.393][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:38.395][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:38.396][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-04-04 16:02:38.397][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:38.399][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:38.400][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:38.401][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:38.401][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:38.401][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:38.401][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:02:38.401][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:02:38.403][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:38.404][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:38.405][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:38.406][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:38.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:38.409][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:38.410][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:38.412][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:38.413][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:38.414][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:38.415][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:38.417][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:38.418][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-04-04 16:02:38.420][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:38.422][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:02:38.423][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:38.424][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:38.426][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:38.427][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:38.428][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:38.429][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:38.431][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:02:38.432][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:38.433][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:38.434][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-04-04 16:02:38.436][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:38.437][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:38.438][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:38.439][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:38.439][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:38.439][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:38.439][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:02:38.439][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:02:38.441][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:38.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:38.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:38.444][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:38.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:38.447][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:38.448][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:38.449][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:38.450][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:38.451][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:38.453][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:38.454][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:38.455][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-04-04 16:02:38.457][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:38.459][self$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[2026-04-04 16:02:38.460][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:38.461][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:38.462][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:38.464][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:38.465][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:38.466][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:38.467][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:02:38.469][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:38.470][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:38.471][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-04-04 16:02:38.472][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:38.474][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:38.475][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:38.476][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:38.477][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:38.479][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:38.480][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:38.481][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:38.482][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:38.484][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:38.485][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:38.486][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:38.487][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:38.488][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:38.490][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:38.491][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:38.492][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-04-04 16:02:38.494][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:38.496][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:02:38.497][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:38.498][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:38.499][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:38.501][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:38.502][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:38.503][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:38.504][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:02:38.506][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:38.507][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:38.509][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-04-04 16:02:38.510][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:38.511][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:38.512][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:38.514][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:38.515][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:38.516][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:38.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:38.518][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:38.520][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:38.521][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:38.522][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:38.523][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:38.524][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:38.525][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:38.527][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:38.528][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:38.532][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:38.533][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.534][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.540][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.546][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.551][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.557][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.563][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.568][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.574][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.580][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.585][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.591][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.596][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.602][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.608][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.613][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.619][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.624][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.626][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-04-04 16:02:38.630][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-04-04 16:02:38.632][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-04-04 16:02:38.638][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-04-04 16:02:38.640][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-04-04 16:02:38.642][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-04-04 16:02:38.644][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-04-04 16:02:38.646][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-04-04 16:02:38.647][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-04-04 16:02:38.649][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-04-04 16:02:38.651][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-04-04 16:02:38.652][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-04-04 16:02:38.654][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-04-04 16:02:38.656][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-04-04 16:02:38.657][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-04-04 16:02:38.659][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-04-04 16:02:38.661][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-04-04 16:02:38.663][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-04-04 16:02:38.664][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-04-04 16:02:38.666][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-04-04 16:02:38.668][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-04-04 16:02:38.669][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-04-04 16:02:38.671][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-04-04 16:02:38.673][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-04-04 16:02:38.675][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-04-04 16:02:38.676][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-04-04 16:02:38.678][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-04-04 16:02:38.680][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-04-04 16:02:38.682][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-04-04 16:02:38.683][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-04-04 16:02:38.685][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-04-04 16:02:38.687][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-04-04 16:02:38.688][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-04-04 16:02:38.690][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-04-04 16:02:38.692][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-04-04 16:02:38.693][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-04-04 16:02:38.695][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-04-04 16:02:38.697][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-04-04 16:02:38.699][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-04-04 16:02:38.700][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-04-04 16:02:38.702][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-04-04 16:02:38.704][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-04-04 16:02:38.705][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-04-04 16:02:38.707][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-04-04 16:02:38.709][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-04-04 16:02:38.711][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-04-04 16:02:38.712][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-04-04 16:02:38.714][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-04-04 16:02:38.716][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-04-04 16:02:38.717][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-04-04 16:02:38.719][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-04-04 16:02:38.721][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-04-04 16:02:38.723][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-04-04 16:02:38.724][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-04-04 16:02:38.726][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-04-04 16:02:38.728][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-04-04 16:02:38.729][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-04-04 16:02:38.731][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-04-04 16:02:38.733][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-04-04 16:02:38.735][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-04-04 16:02:38.736][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-04-04 16:02:38.738][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-04-04 16:02:38.740][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-04-04 16:02:38.741][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-04-04 16:02:38.743][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-04-04 16:02:38.745][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-04-04 16:02:38.747][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-04-04 16:02:38.748][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-04-04 16:02:38.750][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-04-04 16:02:38.752][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-04-04 16:02:38.753][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-04-04 16:02:38.755][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-04-04 16:02:38.757][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-04-04 16:02:38.759][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-04-04 16:02:38.760][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-04-04 16:02:38.762][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-04-04 16:02:38.764][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-04-04 16:02:38.765][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-04-04 16:02:38.767][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-04-04 16:02:38.769][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-04-04 16:02:38.771][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-04-04 16:02:38.772][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-04-04 16:02:38.774][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-04-04 16:02:38.781][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-04-04 16:02:38.784][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:02:38.787][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:38.788][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.791][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.792][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:38.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:38.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.805][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:38.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:38.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:38.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:38.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:38.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.821][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:38.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:38.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.828][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:38.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:38.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:38.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:38.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:38.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.844][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:38.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:38.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:38.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:38.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:38.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.860][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:38.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:38.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.868][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:38.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:38.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:38.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:38.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:38.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.884][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:38.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:38.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.897][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:38.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:38.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:38.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:38.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:38.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.917][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:38.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:38.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.926][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:38.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:38.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.934][FUN] Functions in observer BiodbConfig: [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 [2026-04-04 16:02:38.936][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2026-04-04 16:02:38.946][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2026-04-04 16:02:38.965][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2026-04-04 16:02:38.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:38.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:38.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:38.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:38.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:38.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:38.973][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:38.976][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2026-04-04 16:02:38.989][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2026-04-04 16:02:38.992][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:38.993][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2026-04-04 16:02:38.994][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:38.996][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:38.997][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:38.998][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2026-04-04 16:02:39.000][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:39.001][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:39.002][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-04-04 16:02:39.004][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:39.005][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:39.006][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2026-04-04 16:02:39.008][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:39.009][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2026-04-04 16:02:39.009][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2026-04-04 16:02:39.009][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2026-04-04 16:02:39.009][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2026-04-04 16:02:39.009][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2026-04-04 16:02:39.009][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2026-04-04 16:02:39.009][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2026-04-04 16:02:39.009][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2026-04-04 16:02:39.009][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2026-04-04 16:02:39.009][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2026-04-04 16:02:39.009][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2026-04-04 16:02:39.009][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2026-04-04 16:02:39.009][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2026-04-04 16:02:39.009][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2026-04-04 16:02:39.009][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2026-04-04 16:02:39.009][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2026-04-04 16:02:39.009][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2026-04-04 16:02:39.009][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2026-04-04 16:02:39.011][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:39.012][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:39.012][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2026-04-04 16:02:39.012][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2026-04-04 16:02:39.013][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-04-04 16:02:39.014][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:39.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:39.017][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:39.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:39.019][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:39.020][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:39.022][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2026-04-04 16:02:39.022][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2026-04-04 16:02:39.023][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:39.024][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:39.025][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:39.027][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:39.034][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2026-04-04 16:02:39.036][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-04-04 16:02:39.038][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-04-04 16:02:39.040][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-04-04 16:02:39.042][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-04-04 16:02:39.064][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2026-04-04 16:02:39.080][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2026-04-04 16:02:39.090][biodb::testThat]
biodb.INFO [2026-04-04 16:02:39.091][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-04-04 16:02:39.093][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:39.094][biodb::testThat]
biodb.TRACE[2026-04-04 16:02:39.098][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2026-04-04 16:02:39.100][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2026-04-04 16:02:39.104][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2026-04-04 16:02:39.113][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-04-04 16:02:39.114][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:39.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:39.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:39.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:39.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:39.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-04-04 16:02:39.147][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.148][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.150][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.151][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.185][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:39.187][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:39.188][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.189][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.225][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:39.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:39.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.231][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:39.232][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:39.233][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.235][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.236][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:39.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:39.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.242][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:39.243][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:39.244][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.246][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.247][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:39.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:39.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.253][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:39.254][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:39.255][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.257][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:39.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:39.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.264][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:39.266][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:39.267][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.268][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:39.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:39.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.276][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:39.277][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:39.278][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.280][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.281][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:39.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:39.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.287][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:39.288][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:39.289][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.290][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.292][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:39.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:39.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.298][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:39.299][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:39.300][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.301][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.303][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:39.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:39.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.308][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:39.310][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:39.311][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.312][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.314][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:39.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:39.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.319][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:39.320][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:39.321][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.323][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.324][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:39.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:39.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.329][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:39.331][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:39.332][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.333][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.335][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:39.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:39.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.340][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:39.341][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:39.342][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.344][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.345][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:39.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:39.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.350][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:39.352][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:39.353][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.354][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:39.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:39.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.361][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:39.363][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:39.364][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.365][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.367][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:39.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:39.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.372][ef$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:39.374][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:39.375][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.376][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.378][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:39.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:39.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.383][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:39.385][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:39.386][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.387][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.389][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:39.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:39.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.394][ef$get] Asked field names are: super.class.
biodb.TRACE[2026-04-04 16:02:39.395][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:39.397][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.398][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.400][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2026-04-04 16:02:39.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:39.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.468][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:39.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:39.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.473][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:39.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:39.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.478][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:39.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:39.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.483][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:39.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:39.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.488][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:39.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:39.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.493][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:39.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:39.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:39.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:39.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.503][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:39.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:39.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:39.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:39.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:39.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:39.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:39.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:39.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:39.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:39.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.529][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:39.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:39.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.534][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:39.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:39.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.539][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:39.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:39.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.544][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:39.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:39.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.549][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:39.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:39.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.555][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:39.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:39.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.560][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:39.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:39.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.565][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:39.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:39.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.570][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:39.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:39.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.575][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:39.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:39.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.580][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:39.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:39.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.585][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:39.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:39.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.591][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:39.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:39.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.596][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:39.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:39.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.601][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:39.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:39.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.606][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:39.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:39.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.612][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:39.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:39.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.621][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:39.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:39.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.626][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:39.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:39.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.631][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:39.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:39.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.636][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:39.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:39.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.641][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:39.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:39.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.646][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:39.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:39.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.651][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:39.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:39.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:39.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:39.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:39.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:39.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:39.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:39.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:39.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:39.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:39.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:39.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.681][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:39.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:39.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.686][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:39.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:39.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.691][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:39.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:39.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.696][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:39.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:39.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.701][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:39.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:39.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.706][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:39.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:39.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.711][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:39.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:39.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.716][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:39.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:39.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.721][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:39.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:39.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.726][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:39.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:39.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.731][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-04-04 16:02:39.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:39.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.736][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:39.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:39.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.741][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:39.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:39.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.746][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:39.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:39.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.751][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-04-04 16:02:39.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:39.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.780][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:39.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:39.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.785][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:39.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:39.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:39.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:39.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:39.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:39.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.800][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:39.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:39.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.805][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:39.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:39.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.810][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:39.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:39.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.820][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:39.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:39.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-04-04 16:02:39.890][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2026-04-04 16:02:39.893][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:02:39.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:02:39.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.898][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:02:39.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:02:39.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.903][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-04-04 16:02:39.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-04-04 16:02:39.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.908][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-04-04 16:02:39.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-04-04 16:02:39.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.924][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:39.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:39.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.968][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:39.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:39.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.973][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:39.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:39.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.978][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:39.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:39.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:39.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:39.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:39.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:39.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:40.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:40.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.007][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:40.008][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:40.010][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.011][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:40.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:40.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.028][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:40.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:40.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.033][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:40.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:40.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.038][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:40.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:40.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.043][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:40.045][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:40.046][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.047][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.048][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:40.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:40.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:40.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:40.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:40.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:40.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:40.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:40.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.079][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:40.080][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:40.081][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.083][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:40.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:40.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.103][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:40.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:40.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.108][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:40.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:40.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.113][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:40.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:40.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.118][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:40.119][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:40.121][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.122][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.123][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:40.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:40.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:40.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:40.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:40.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:40.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:40.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:40.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.153][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:40.155][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:40.156][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.157][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:40.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:40.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.173][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:40.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:40.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.178][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:40.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:40.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.183][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:40.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:40.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.188][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:40.189][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:40.190][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.192][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.193][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:40.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:40.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.208][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:40.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:40.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.213][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:40.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:40.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.219][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:40.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:40.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.224][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:40.225][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:40.226][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.228][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.229][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:40.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:40.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.244][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:40.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:40.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.250][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:40.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:40.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.255][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:40.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:40.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.260][ef$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:40.261][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:40.262][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.263][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.265][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:40.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:40.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.280][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:40.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:40.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.285][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:40.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:40.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.290][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:40.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:40.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.296][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:40.297][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:40.298][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.299][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.301][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:40.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:40.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.320][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:40.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:40.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.325][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:40.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:40.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.330][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:40.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:40.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.335][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:40.336][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:40.337][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.339][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.340][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:40.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:40.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:40.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:40.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.360][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:40.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:40.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.365][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:40.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:40.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.370][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:40.372][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:40.373][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.374][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:40.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:40.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.390][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:40.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:40.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.395][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:40.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:40.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.400][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:40.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:40.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.405][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:40.406][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:40.407][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.409][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.410][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:40.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:40.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.425][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:40.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:40.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.430][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:40.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:40.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.435][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:40.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:40.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.440][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:40.441][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:40.442][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.443][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.445][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:40.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:40.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.460][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:40.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:40.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.465][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:40.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:40.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.470][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:40.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:40.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.475][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:40.476][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:40.477][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.479][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.480][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:40.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:40.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.495][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:40.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:40.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.500][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:40.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:40.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.505][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:40.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:40.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.510][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:40.511][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:40.513][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.514][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.515][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:40.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:40.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.535][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:40.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:40.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.540][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:40.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:40.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:40.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:40.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.550][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:40.551][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:40.553][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.554][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.555][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:40.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:40.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:40.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:40.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:40.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:40.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:40.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:40.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.585][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:40.587][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:40.588][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.589][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.590][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:40.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:40.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.605][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:40.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:40.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.610][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:40.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:40.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.615][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:40.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:40.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.620][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:40.622][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:40.623][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.624][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.625][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:40.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:40.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.640][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:40.642][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:40.643][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.644][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.651][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:40.652][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:40.654][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.655][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.661][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:40.662][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:40.664][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.665][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.671][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:40.673][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:40.674][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.675][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.681][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:40.683][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:40.684][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.685][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.692][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:40.693][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:40.695][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.696][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.702][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:40.704][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:40.706][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.707][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.714][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:40.715][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:40.717][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.718][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.725][ef$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:40.726][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:40.728][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.729][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.735][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:40.738][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:40.739][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.740][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.747][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:40.748][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:40.750][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.751][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.757][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:40.759][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:40.760][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.761][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.772][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:40.774][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:40.775][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.776][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.784][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:40.786][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:40.788][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.789][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.796][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:40.797][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:40.798][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.800][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.806][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:40.808][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:40.809][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.811][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.818][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:40.820][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:40.821][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.822][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:40.829][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:40.831][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:40.832][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:40.834][ef$get] fields variable is a list.
biodb.INFO [2026-04-04 16:02:40.844][biodb::testThat]
biodb.INFO [2026-04-04 16:02:40.846][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-04-04 16:02:40.847][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:40.848][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:40.868][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-04-04 16:02:40.873][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-04-04 16:02:40.877][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-04-04 16:02:40.926][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-04-04 16:02:40.928][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-04-04 16:02:40.929][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-04-04 16:02:41.132][biodb::testThat]
biodb.INFO [2026-04-04 16:02:41.133][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-04-04 16:02:41.134][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:41.135][biodb::testThat]
biodb.TRACE[2026-04-04 16:02:41.139][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:41.141][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:41.142][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:41.143][ef$get] fields variable is a list.
biodb.DEBUG[2026-04-04 16:02:41.145][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2026-04-04 16:02:41.175][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-04-04 16:02:41.245][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-04-04 16:02:41.247][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-04-04 16:02:41.249][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-04-04 16:02:41.251][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-04-04 16:02:41.268][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-04-04 16:02:41.339][biodb::testThat]
biodb.INFO [2026-04-04 16:02:41.340][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-04-04 16:02:41.341][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:41.342][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:41.353][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-04-04 16:02:41.354][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-04-04 16:02:41.356][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-04-04 16:02:41.357][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-04-04 16:02:41.359][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-04-04 16:02:41.360][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-04-04 16:02:41.421][biodb::testThat]
biodb.INFO [2026-04-04 16:02:41.422][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-04-04 16:02:41.423][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:41.424][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:41.430][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-04-04 16:02:41.431][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-04-04 16:02:41.433][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-04-04 16:02:41.435][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-04-04 16:02:41.436][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-04-04 16:02:41.438][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-04-04 16:02:41.502][biodb::testThat]
biodb.INFO [2026-04-04 16:02:41.504][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-04-04 16:02:41.507][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:41.508][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-04-04 16:02:41.576][biodb::testThat]
biodb.INFO [2026-04-04 16:02:41.577][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-04-04 16:02:41.578][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:41.579][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-04-04 16:02:41.668][biodb::testThat]
biodb.INFO [2026-04-04 16:02:41.670][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-04-04 16:02:41.673][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:41.674][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-04-04 16:02:41.737][biodb::testThat]
biodb.INFO [2026-04-04 16:02:41.738][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-04-04 16:02:41.740][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:41.741][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2026-04-04 16:02:41.844][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:41.846][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:41.848][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:41.850][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:41.852][ef$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:41.854][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:41.856][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:41.858][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:41.860][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:41.863][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:41.865][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:41.867][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:41.870][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:41.872][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:41.875][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:41.877][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:41.879][ef$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:41.882][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:41.884][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:41.886][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:41.889][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:41.891][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:41.893][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:41.895][ef$get] fields variable is a list.
biodb.INFO [2026-04-04 16:02:41.898][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-04-04 16:02:41.900][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2026-04-04 16:02:41.902][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-04-04 16:02:41.904][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:41.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:41.907][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:41.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:41.909][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:41.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]

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

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

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

'R CMD check' output

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


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

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

Installation output

biodbHmdb.Rcheck/00install.out

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