Back to Long Tests report for BioC 3.22

This page was generated on 2025-11-29 23:55 -0500 (Sat, 29 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4878
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4624
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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

CHECK results for biodbHmdb on nebbiolo2

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

raw results


Summary

Package: biodbHmdb
Version: 1.16.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
StartedAt: 2025-11-29 16:01:23 -0500 (Sat, 29 Nov 2025)
EndedAt: 2025-11-29 16:02:32 -0500 (Sat, 29 Nov 2025)
EllapsedTime: 69.0 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"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-11-29 16:02:28.077][biodb::testContext]
biodb.INFO [2025-11-29 16:02:28.079][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-29 16:02:28.080][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-11-29 16:02:28.081][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-29 16:02:28.082][biodb::testContext]
biodb.INFO [2025-11-29 16:02:28.088][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-29 16:02:28.089][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-11-29 16:02:28.096][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-29 16:02:28.097][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-29 16:02:28.098][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-29 16:02:28.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.102][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-29 16:02:28.118][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-29 16:02:28.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.121][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-29 16:02:28.122][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-29 16:02:28.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.134][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-29 16:02:28.135][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-29 16:02:28.136][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-29 16:02:28.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.139][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-29 16:02:28.140][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-29 16:02:28.141][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-29 16:02:28.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.144][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-29 16:02:28.145][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-29 16:02:28.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.149][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-29 16:02:28.150][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-29 16:02:28.151][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-29 16:02:28.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.154][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-29 16:02:28.155][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-29 16:02:28.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.158][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-29 16:02:28.159][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-29 16:02:28.160][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-29 16:02:28.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.164][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-29 16:02:28.164][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-29 16:02:28.165][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-29 16:02:28.166][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-29 16:02:28.167][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-29 16:02:28.168][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-29 16:02:28.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.171][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-29 16:02:28.172][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-29 16:02:28.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.176][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-29 16:02:28.177][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-29 16:02:28.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.180][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-29 16:02:28.181][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-29 16:02:28.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.184][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-29 16:02:28.185][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-29 16:02:28.186][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-29 16:02:28.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.190][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-29 16:02:28.191][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-29 16:02:28.194][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-29 16:02:28.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.197][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-29 16:02:28.198][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-29 16:02:28.199][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-29 16:02:28.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.205][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-29 16:02:28.235][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:28.249][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-11-29 16:02:28.250][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.251][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-29 16:02:28.252][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.253][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-29 16:02:28.254][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:28.255][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-29 16:02:28.256][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-29 16:02:28.257][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-29 16:02:28.258][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.259][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-29 16:02:28.259][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-29 16:02:28.260][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:28.261][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.262][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-29 16:02:28.262][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-29 16:02:28.262][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-29 16:02:28.262][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-29 16:02:28.262][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-29 16:02:28.263][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-29 16:02:28.264][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:28.265][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:28.266][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-29 16:02:28.267][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:28.267][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:28.268][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-29 16:02:28.269][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:28.270][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-29 16:02:28.271][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-29 16:02:28.272][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:28.273][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:28.274][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-29 16:02:28.275][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:28.276][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-29 16:02:28.277][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.278][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-29 16:02:28.279][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.280][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-29 16:02:28.281][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:28.286][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-29 16:02:28.287][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-29 16:02:28.288][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-29 16:02:28.289][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.290][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-29 16:02:28.290][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-29 16:02:28.291][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:28.292][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.293][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-29 16:02:28.293][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-29 16:02:28.293][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-29 16:02:28.293][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-29 16:02:28.293][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-29 16:02:28.294][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-29 16:02:28.295][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:28.296][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:28.297][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-29 16:02:28.298][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:28.298][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:28.299][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-29 16:02:28.300][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:28.301][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-29 16:02:28.302][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-29 16:02:28.303][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:28.304][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:28.305][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-29 16:02:28.306][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.307][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-11-29 16:02:28.308][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.309][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-29 16:02:28.310][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.311][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-29 16:02:28.312][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:28.313][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-29 16:02:28.314][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-29 16:02:28.315][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-29 16:02:28.316][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:28.317][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-29 16:02:28.318][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-29 16:02:28.318][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:28.319][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.320][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:28.321][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-29 16:02:28.322][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:28.323][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:28.324][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-29 16:02:28.325][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:28.326][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:28.326][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-29 16:02:28.327][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:28.328][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-29 16:02:28.329][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-29 16:02:28.330][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:28.331][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:28.332][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-29 16:02:28.333][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.334][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-29 16:02:28.335][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.336][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-29 16:02:28.337][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.338][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-29 16:02:28.339][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:28.340][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-29 16:02:28.341][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-29 16:02:28.342][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-29 16:02:28.343][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:28.344][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-29 16:02:28.345][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-29 16:02:28.345][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:28.346][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.347][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:28.348][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-29 16:02:28.349][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:28.350][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:28.351][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-29 16:02:28.352][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:28.352][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:28.353][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-29 16:02:28.354][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:28.355][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-29 16:02:28.356][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-29 16:02:28.357][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:28.358][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:28.361][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-29 16:02:28.362][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.430][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-29 16:02:28.434][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-29 16:02:28.435][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-29 16:02:28.437][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-29 16:02:28.438][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-29 16:02:28.443][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-29 16:02:28.444][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-29 16:02:28.446][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-29 16:02:28.447][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-29 16:02:28.448][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-29 16:02:28.449][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-29 16:02:28.451][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-29 16:02:28.452][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-29 16:02:28.453][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-29 16:02:28.455][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-29 16:02:28.456][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-29 16:02:28.457][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-29 16:02:28.458][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-29 16:02:28.460][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-29 16:02:28.461][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-29 16:02:28.462][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-29 16:02:28.464][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-29 16:02:28.465][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-29 16:02:28.466][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-29 16:02:28.468][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-29 16:02:28.469][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-29 16:02:28.470][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-29 16:02:28.471][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-29 16:02:28.473][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-29 16:02:28.474][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-29 16:02:28.475][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-29 16:02:28.477][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-29 16:02:28.478][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-29 16:02:28.479][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-29 16:02:28.480][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-29 16:02:28.482][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-29 16:02:28.483][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-29 16:02:28.484][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-29 16:02:28.486][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-29 16:02:28.487][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-29 16:02:28.488][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-29 16:02:28.489][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-29 16:02:28.491][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-29 16:02:28.492][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-29 16:02:28.493][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-29 16:02:28.501][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-29 16:02:28.504][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-29 16:02:28.505][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-29 16:02:28.507][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-29 16:02:28.508][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-29 16:02:28.510][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-29 16:02:28.511][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-29 16:02:28.513][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-29 16:02:28.514][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-29 16:02:28.515][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-29 16:02:28.517][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-29 16:02:28.518][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-29 16:02:28.520][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-29 16:02:28.521][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-29 16:02:28.523][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-29 16:02:28.524][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-29 16:02:28.526][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-29 16:02:28.527][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-29 16:02:28.528][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-29 16:02:28.530][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-29 16:02:28.531][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-29 16:02:28.533][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-29 16:02:28.534][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-29 16:02:28.536][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-29 16:02:28.537][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-29 16:02:28.538][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-29 16:02:28.540][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-29 16:02:28.541][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-29 16:02:28.543][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-29 16:02:28.544][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-29 16:02:28.546][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-29 16:02:28.547][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-29 16:02:28.548][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-29 16:02:28.550][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-29 16:02:28.551][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-29 16:02:28.553][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-29 16:02:28.554][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-29 16:02:28.556][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-29 16:02:28.563][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-29 16:02:28.565][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-29 16:02:28.568][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-29 16:02:28.569][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.571][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:28.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:28.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:28.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:28.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:28.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:28.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:28.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:28.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.602][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[2025-11-29 16:02:28.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:28.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:28.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.608][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[2025-11-29 16:02:28.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:28.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:28.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:28.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:28.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:28.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:28.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:28.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:28.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:28.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:28.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:28.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:28.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:28.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:28.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:28.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:28.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:28.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:28.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:28.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:28.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:28.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:28.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2025-11-29 16:02:28.690][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-11-29 16:02:28.698][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-11-29 16:02:28.711][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-11-29 16:02:28.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:28.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:28.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:28.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:28.719][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-11-29 16:02:28.727][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-11-29 16:02:28.729][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:28.730][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-11-29 16:02:28.731][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.732][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-29 16:02:28.733][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:28.734][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-11-29 16:02:28.735][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.736][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-29 16:02:28.736][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-29 16:02:28.737][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-29 16:02:28.738][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.739][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-11-29 16:02:28.740][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-29 16:02:28.741][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-11-29 16:02:28.741][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-11-29 16:02:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-11-29 16:02:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-11-29 16:02:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-11-29 16:02:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-11-29 16:02:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-11-29 16:02:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-11-29 16:02:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-11-29 16:02:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-11-29 16:02:28.741][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-11-29 16:02:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-11-29 16:02:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-11-29 16:02:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-11-29 16:02:28.741][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-11-29 16:02:28.741][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-11-29 16:02:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-11-29 16:02:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-11-29 16:02:28.742][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:28.743][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-29 16:02:28.743][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-11-29 16:02:28.743][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-11-29 16:02:28.744][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-29 16:02:28.745][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:28.746][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:28.747][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-29 16:02:28.747][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:28.748][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:28.749][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-29 16:02:28.750][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-11-29 16:02:28.750][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-11-29 16:02:28.751][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-29 16:02:28.752][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-29 16:02:28.753][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:28.754][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:28.759][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-11-29 16:02:28.760][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-29 16:02:28.762][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-29 16:02:28.763][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-29 16:02:28.765][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-29 16:02:28.789][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-11-29 16:02:28.803][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-11-29 16:02:28.810][biodb::testThat]
biodb.INFO [2025-11-29 16:02:28.811][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-29 16:02:28.812][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-29 16:02:28.813][biodb::testThat]
biodb.TRACE[2025-11-29 16:02:28.817][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-11-29 16:02:28.818][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-11-29 16:02:28.821][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-11-29 16:02:28.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-29 16:02:28.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:28.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:28.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:28.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:28.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:28.844][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.TRACE[2025-11-29 16:02:28.855][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:28.856][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:28.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.857][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:28.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:28.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.874][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:28.875][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:28.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.877][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.901][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:28.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:28.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.905][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:28.906][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:28.907][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.907][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.909][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:28.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:28.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.912][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:28.913][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:28.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.915][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.916][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:28.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:28.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.920][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:28.921][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:28.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.923][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:28.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:28.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.928][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:28.929][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:28.930][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.931][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:28.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:28.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.945][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:28.946][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:28.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.947][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.949][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:28.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:28.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.952][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:28.953][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:28.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.955][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.956][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:28.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:28.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.960][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:28.961][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:28.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.963][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.964][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:28.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:28.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.968][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:28.969][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:28.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.971][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.972][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:28.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:28.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.976][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:28.977][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:28.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.978][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.979][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:28.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:28.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.983][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:28.984][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:28.985][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.986][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.987][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:28.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:28.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.991][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:28.992][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:28.993][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.994][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.995][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:28.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:28.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:28.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:28.999][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.000][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.000][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.001][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.006][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:29.007][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:29.008][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.009][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.010][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:29.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:29.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.014][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:29.015][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:29.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.016][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.018][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:29.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:29.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.021][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:29.022][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:29.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.024][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.025][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:29.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:29.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.029][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-11-29 16:02:29.030][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:29.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.032][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.033][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-11-29 16:02:29.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:29.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.120][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:29.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:29.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.124][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:29.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:29.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.128][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:29.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:29.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.132][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:29.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:29.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.135][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:29.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:29.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.139][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:29.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:29.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:29.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:29.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:29.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:29.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:29.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:29.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:29.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:29.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:29.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:29.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:29.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:29.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.165][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:29.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:29.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.169][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:29.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:29.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.172][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:29.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:29.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.176][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:29.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:29.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.180][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:29.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:29.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.183][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:29.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:29.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.187][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:29.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:29.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.191][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:29.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:29.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.194][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:29.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:29.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.198][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:29.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:29.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.201][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:29.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:29.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.205][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:29.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:29.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.209][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:29.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:29.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.212][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:29.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:29.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.220][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:29.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:29.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.223][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:29.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:29.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.227][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:29.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:29.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:29.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:29.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.234][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.238][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.245][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:29.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:29.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.249][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:29.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:29.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.253][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:29.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:29.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:29.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:29.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:29.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:29.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.275][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:29.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:29.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.279][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:29.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:29.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.282][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:29.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:29.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.286][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:29.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:29.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.290][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:29.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:29.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.293][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:29.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:29.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.297][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:29.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:29.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.301][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:29.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:29.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.304][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:29.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:29.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.308][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:29.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:29.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.312][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-11-29 16:02:29.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.315][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.319][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.322][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.326][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-11-29 16:02:29.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.350][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:29.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:29.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.354][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:29.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:29.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.357][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:29.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:29.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.361][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:29.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:29.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.365][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:29.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:29.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.369][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:29.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:29.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.372][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:29.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:29.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.380][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:29.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:29.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-29 16:02:29.406][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-11-29 16:02:29.408][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-29 16:02:29.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-29 16:02:29.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.412][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-29 16:02:29.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-29 16:02:29.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.415][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-29 16:02:29.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-29 16:02:29.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.419][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-29 16:02:29.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-29 16:02:29.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.431][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:29.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:29.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.466][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:29.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:29.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.470][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:29.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:29.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.474][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:29.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:29.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.494][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.495][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.497][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:29.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:29.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.510][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:29.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:29.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.514][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:29.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:29.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.518][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:29.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:29.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.522][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:29.523][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:29.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.525][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.526][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:29.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:29.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:29.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:29.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:29.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:29.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:29.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:29.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.550][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:29.551][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:29.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.553][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:29.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:29.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.566][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:29.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:29.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.570][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:29.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:29.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.574][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:29.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:29.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.578][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:29.579][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:29.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.581][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.582][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:29.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:29.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:29.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:29.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:29.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:29.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:29.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:29.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.612][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:29.613][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:29.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.615][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:29.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:29.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.628][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:29.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:29.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.632][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:29.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:29.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.636][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:29.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:29.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.640][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:29.642][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:29.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.643][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.644][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:29.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:29.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.656][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:29.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:29.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.660][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:29.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:29.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.664][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:29.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:29.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.668][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:29.669][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:29.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.671][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:29.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:29.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.684][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:29.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:29.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.688][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:29.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:29.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.692][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:29.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:29.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.696][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:29.697][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:29.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.699][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.700][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:29.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:29.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.711][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:29.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:29.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.715][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:29.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:29.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.725][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:29.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:29.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.729][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:29.730][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:29.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.732][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.733][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:29.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:29.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.745][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:29.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:29.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.749][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:29.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:29.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.753][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:29.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:29.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.757][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:29.758][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:29.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.760][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.761][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:29.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:29.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.785][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.786][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.788][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:29.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.801][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:29.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:29.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.805][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:29.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:29.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.809][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:29.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:29.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.813][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:29.814][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:29.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.816][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.817][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:29.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:29.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.829][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:29.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:29.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.833][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:29.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:29.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.837][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:29.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:29.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.841][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:29.842][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:29.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.844][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.845][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:29.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:29.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.863][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:29.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:29.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.867][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:29.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:29.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.871][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:29.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:29.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.875][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:29.876][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:29.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.878][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.879][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:29.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:29.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.891][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:29.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:29.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.895][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:29.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:29.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.899][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:29.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:29.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.903][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:29.904][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:29.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.906][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.907][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:29.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:29.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.919][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:29.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:29.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.923][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:29.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:29.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.928][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:29.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:29.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.932][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:29.933][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:29.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.935][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.936][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:29.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:29.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.947][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.951][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.955][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.959][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.961][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.962][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.963][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:29.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.975][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:29.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:29.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.979][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:29.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:29.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.988][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:29.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:29.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.992][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:29.993][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:29.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.995][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:29.996][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:29.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:29.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:29.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.008][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:30.009][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:30.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.011][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.015][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:30.016][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:30.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.018][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.022][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:30.024][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:30.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.025][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.030][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:30.031][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:30.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.033][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.037][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:30.038][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:30.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.040][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.044][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:30.045][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:30.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.047][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.051][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:30.052][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:30.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.054][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.058][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:30.059][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:30.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.061][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.065][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:30.066][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:30.067][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.068][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.072][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:30.074][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:30.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.075][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.080][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:30.081][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:30.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.083][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.087][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:30.088][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:30.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.090][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.094][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:30.095][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:30.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.097][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.101][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:30.102][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:30.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.104][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.108][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:30.109][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:30.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.111][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.121][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:30.122][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:30.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.124][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.128][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:30.129][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:30.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.131][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.136][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:30.137][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:30.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.139][ef$get] fields variable is a list.
biodb.INFO [2025-11-29 16:02:30.146][biodb::testThat]
biodb.INFO [2025-11-29 16:02:30.147][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-29 16:02:30.148][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-29 16:02:30.148][biodb::testThat]
biodb.DEBUG[2025-11-29 16:02:30.163][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-29 16:02:30.165][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-29 16:02:30.169][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-29 16:02:30.199][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-29 16:02:30.200][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-29 16:02:30.201][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-29 16:02:30.343][biodb::testThat]
biodb.INFO [2025-11-29 16:02:30.344][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-29 16:02:30.345][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-29 16:02:30.346][biodb::testThat]
biodb.TRACE[2025-11-29 16:02:30.357][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:30.358][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:30.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.360][ef$get] fields variable is a list.
biodb.DEBUG[2025-11-29 16:02:30.361][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-11-29 16:02:30.384][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-29 16:02:30.430][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-29 16:02:30.432][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-29 16:02:30.434][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-29 16:02:30.435][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-29 16:02:30.448][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-29 16:02:30.509][biodb::testThat]
biodb.INFO [2025-11-29 16:02:30.511][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-29 16:02:30.512][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-29 16:02:30.513][biodb::testThat]
biodb.DEBUG[2025-11-29 16:02:30.520][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-29 16:02:30.521][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-29 16:02:30.522][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-29 16:02:30.524][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-29 16:02:30.525][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-29 16:02:30.526][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-29 16:02:30.576][biodb::testThat]
biodb.INFO [2025-11-29 16:02:30.577][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-29 16:02:30.578][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-29 16:02:30.579][biodb::testThat]
biodb.DEBUG[2025-11-29 16:02:30.583][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-29 16:02:30.584][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-29 16:02:30.586][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-29 16:02:30.587][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-29 16:02:30.588][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-29 16:02:30.589][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-29 16:02:30.634][biodb::testThat]
biodb.INFO [2025-11-29 16:02:30.636][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-29 16:02:30.637][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-29 16:02:30.638][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-29 16:02:30.689][biodb::testThat]
biodb.INFO [2025-11-29 16:02:30.690][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-29 16:02:30.691][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-29 16:02:30.692][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-29 16:02:30.737][biodb::testThat]
biodb.INFO [2025-11-29 16:02:30.738][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-29 16:02:30.739][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-29 16:02:30.740][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-29 16:02:30.792][biodb::testThat]
biodb.INFO [2025-11-29 16:02:30.793][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-29 16:02:30.794][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-29 16:02:30.795][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2025-11-29 16:02:30.852][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:30.854][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:30.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.856][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.857][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:30.858][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:30.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.860][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.861][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:30.862][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:30.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.864][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.865][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:30.866][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:30.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.868][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.869][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:30.870][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:30.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.872][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:30.873][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:30.874][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:30.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:30.876][ef$get] fields variable is a list.
biodb.INFO [2025-11-29 16:02:30.877][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-29 16:02:30.884][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-11-29 16:02:30.884][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-29 16:02:30.885][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:30.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:30.887][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:30.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:30.889][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:30.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]

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

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
   5.       └─base::vapply(id, fct, FUN.VALUE = "")
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  
  [ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

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

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.16.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor ‘EntryMaker::EntryMaker()’:
EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)