Back to Long Tests report for BioC 3.22

This page was generated on 2025-08-02 23:55 -0400 (Sat, 02 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4535
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 6/29HostnameOS / ArchCHECK
biodbHmdb 1.15.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-08-02 09:55 -0400 (Sat, 02 Aug 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: fa89c02
git_last_commit_date: 2025-07-24 10:45:35 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  ERROR  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 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: 1.15.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.15.1.tar.gz
StartedAt: 2025-08-02 16:01:06 -0400 (Sat, 02 Aug 2025)
EndedAt: 2025-08-02 16:02:09 -0400 (Sat, 02 Aug 2025)
EllapsedTime: 63.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 (2025-06-13) -- "Great Square Root"
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 [2025-08-02 16:02:06.191][biodb::testContext]
biodb.INFO [2025-08-02 16:02:06.193][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-02 16:02:06.194][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-08-02 16:02:06.195][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-02 16:02:06.196][biodb::testContext]
biodb.INFO [2025-08-02 16:02:06.201][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-02 16:02:06.203][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-02 16:02:06.210][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-02 16:02:06.211][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-02 16:02:06.212][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-02 16:02:06.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-02 16:02:06.215][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-02 16:02:06.232][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-02 16:02:06.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.235][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.236][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-02 16:02:06.237][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-02 16:02:06.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-02 16:02:06.240][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-02 16:02:06.241][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-02 16:02:06.242][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-02 16:02:06.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-02 16:02:06.245][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-02 16:02:06.246][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-02 16:02:06.247][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-02 16:02:06.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-02 16:02:06.251][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-02 16:02:06.252][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-02 16:02:06.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.254][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.255][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-02 16:02:06.256][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-02 16:02:06.257][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-02 16:02:06.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-02 16:02:06.261][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-02 16:02:06.262][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-02 16:02:06.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.264][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.265][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-02 16:02:06.266][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-02 16:02:06.267][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-02 16:02:06.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-02 16:02:06.270][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-02 16:02:06.271][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-02 16:02:06.272][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-02 16:02:06.273][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-02 16:02:06.274][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-02 16:02:06.275][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-02 16:02:06.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.278][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.279][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-02 16:02:06.280][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-02 16:02:06.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-02 16:02:06.283][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-02 16:02:06.284][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-02 16:02:06.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.287][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.287][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-02 16:02:06.288][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-02 16:02:06.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-02 16:02:06.292][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-02 16:02:06.293][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-02 16:02:06.294][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-02 16:02:06.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.296][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.297][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-02 16:02:06.298][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-02 16:02:06.302][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-02 16:02:06.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-02 16:02:06.306][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-02 16:02:06.307][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-02 16:02:06.308][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-02 16:02:06.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.315][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.318][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-02 16:02:06.349][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-02 16:02:06.364][self$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[2025-08-02 16:02:06.365][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.366][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-02 16:02:06.367][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.368][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-02 16:02:06.369][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-02 16:02:06.370][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-02 16:02:06.371][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-02 16:02:06.372][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-02 16:02:06.372][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.373][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-02 16:02:06.374][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-02 16:02:06.375][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-02 16:02:06.376][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.377][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-02 16:02:06.377][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-02 16:02:06.377][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-02 16:02:06.377][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-02 16:02:06.377][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-02 16:02:06.378][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-02 16:02:06.379][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-02 16:02:06.380][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-02 16:02:06.381][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-02 16:02:06.382][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-02 16:02:06.383][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-02 16:02:06.383][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-02 16:02:06.384][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-02 16:02:06.385][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-02 16:02:06.386][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-02 16:02:06.387][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-02 16:02:06.388][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-02 16:02:06.389][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-02 16:02:06.391][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-02 16:02:06.392][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-02 16:02:06.393][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.394][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-02 16:02:06.394][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.395][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-02 16:02:06.396][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-02 16:02:06.397][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-02 16:02:06.398][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-02 16:02:06.399][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-02 16:02:06.400][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.401][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-02 16:02:06.402][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-02 16:02:06.403][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-02 16:02:06.404][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.405][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-02 16:02:06.405][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-02 16:02:06.405][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-02 16:02:06.405][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-02 16:02:06.405][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-02 16:02:06.406][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-02 16:02:06.407][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-02 16:02:06.407][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-02 16:02:06.408][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-02 16:02:06.409][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-02 16:02:06.410][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-02 16:02:06.411][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-02 16:02:06.412][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-02 16:02:06.413][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-02 16:02:06.414][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-02 16:02:06.414][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-02 16:02:06.415][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-02 16:02:06.416][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-02 16:02:06.418][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.419][self$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[2025-08-02 16:02:06.420][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.421][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-02 16:02:06.422][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.423][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-02 16:02:06.424][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-02 16:02:06.425][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-02 16:02:06.426][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-02 16:02:06.427][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-02 16:02:06.427][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-02 16:02:06.428][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-02 16:02:06.429][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-02 16:02:06.430][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-02 16:02:06.431][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.432][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-02 16:02:06.433][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-02 16:02:06.434][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-02 16:02:06.435][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-02 16:02:06.436][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-02 16:02:06.437][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-02 16:02:06.437][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-02 16:02:06.438][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-02 16:02:06.439][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-02 16:02:06.440][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-02 16:02:06.441][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-02 16:02:06.442][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-02 16:02:06.443][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-02 16:02:06.444][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-02 16:02:06.446][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.447][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-02 16:02:06.448][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.449][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-02 16:02:06.450][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.451][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-02 16:02:06.451][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-02 16:02:06.452][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-02 16:02:06.453][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-02 16:02:06.454][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-02 16:02:06.455][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-02 16:02:06.456][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-02 16:02:06.457][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-02 16:02:06.458][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-02 16:02:06.459][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.460][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-02 16:02:06.461][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-02 16:02:06.462][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-02 16:02:06.463][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-02 16:02:06.464][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-02 16:02:06.465][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-02 16:02:06.465][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-02 16:02:06.466][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-02 16:02:06.467][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-02 16:02:06.468][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-02 16:02:06.469][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-02 16:02:06.470][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-02 16:02:06.471][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-02 16:02:06.479][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-02 16:02:06.480][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.481][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-02 16:02:06.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.489][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.493][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.498][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.502][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.506][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.510][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.514][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.518][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.523][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.527][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.531][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.535][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.539][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.543][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.548][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.549][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-02 16:02:06.553][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-02 16:02:06.554][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-02 16:02:06.556][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-02 16:02:06.557][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-02 16:02:06.558][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-02 16:02:06.560][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-02 16:02:06.561][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-02 16:02:06.562][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-02 16:02:06.563][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-02 16:02:06.565][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-02 16:02:06.566][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-02 16:02:06.567][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-02 16:02:06.569][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-02 16:02:06.570][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-02 16:02:06.571][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-02 16:02:06.573][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-02 16:02:06.574][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-02 16:02:06.575][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-02 16:02:06.576][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-02 16:02:06.578][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-02 16:02:06.579][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-02 16:02:06.580][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-02 16:02:06.582][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-02 16:02:06.583][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-02 16:02:06.584][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-02 16:02:06.586][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-02 16:02:06.587][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-02 16:02:06.588][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-02 16:02:06.590][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-02 16:02:06.591][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-02 16:02:06.592][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-02 16:02:06.594][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-02 16:02:06.595][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-02 16:02:06.596][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-02 16:02:06.598][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-02 16:02:06.599][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-02 16:02:06.600][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-02 16:02:06.601][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-02 16:02:06.603][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-02 16:02:06.604][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-02 16:02:06.605][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-02 16:02:06.607][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-02 16:02:06.608][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-02 16:02:06.609][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-02 16:02:06.611][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-02 16:02:06.612][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-02 16:02:06.613][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-02 16:02:06.615][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-02 16:02:06.616][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-02 16:02:06.617][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-02 16:02:06.619][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-02 16:02:06.620][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-02 16:02:06.621][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-02 16:02:06.623][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-02 16:02:06.624][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-02 16:02:06.625][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-02 16:02:06.626][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-02 16:02:06.628][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-02 16:02:06.629][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-02 16:02:06.630][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-02 16:02:06.632][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-02 16:02:06.633][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-02 16:02:06.634][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-02 16:02:06.635][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-02 16:02:06.637][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-02 16:02:06.638][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-02 16:02:06.639][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-02 16:02:06.644][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-02 16:02:06.646][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-02 16:02:06.647][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-02 16:02:06.648][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-02 16:02:06.650][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-02 16:02:06.651][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-02 16:02:06.652][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-02 16:02:06.653][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-02 16:02:06.655][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-02 16:02:06.656][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-02 16:02:06.657][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-02 16:02:06.659][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-02 16:02:06.660][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-02 16:02:06.661][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-02 16:02:06.662][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-02 16:02:06.668][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-02 16:02:06.669][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-02 16:02:06.672][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-02 16:02:06.673][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.675][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-02 16:02:06.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:06.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:06.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.685][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:06.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:06.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.691][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:06.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:06.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.696][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:06.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:06.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.702][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:06.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:06.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.708][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:06.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:06.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.714][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:06.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:06.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.720][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:06.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:06.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.725][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:06.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:06.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.731][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:06.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:06.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.738][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:06.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:06.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.744][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:06.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:06.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.749][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:06.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:06.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.755][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:06.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:06.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.761][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:06.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:06.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-02 16:02:06.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:06.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:06.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2025-08-02 16:02:06.782][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-08-02 16:02:06.794][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-08-02 16:02:06.809][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-02 16:02:06.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-02 16:02:06.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:06.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:06.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.827][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.829][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-08-02 16:02:06.839][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-08-02 16:02:06.841][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-02 16:02:06.842][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-02 16:02:06.843][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.844][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-02 16:02:06.845][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-08-02 16:02:06.846][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-08-02 16:02:06.847][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.848][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-02 16:02:06.849][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-02 16:02:06.850][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-02 16:02:06.851][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.852][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-08-02 16:02:06.853][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-02 16:02:06.854][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-08-02 16:02:06.854][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-08-02 16:02:06.854][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-08-02 16:02:06.854][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-08-02 16:02:06.854][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-08-02 16:02:06.854][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-08-02 16:02:06.854][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-08-02 16:02:06.854][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-08-02 16:02:06.854][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-08-02 16:02:06.854][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-08-02 16:02:06.854][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-08-02 16:02:06.854][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-08-02 16:02:06.854][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-08-02 16:02:06.854][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-08-02 16:02:06.854][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-08-02 16:02:06.854][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-08-02 16:02:06.854][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-08-02 16:02:06.854][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-08-02 16:02:06.855][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-02 16:02:06.856][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-02 16:02:06.856][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-08-02 16:02:06.856][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-08-02 16:02:06.857][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-02 16:02:06.858][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-02 16:02:06.859][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-02 16:02:06.860][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-02 16:02:06.861][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-02 16:02:06.862][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-02 16:02:06.863][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-02 16:02:06.864][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-08-02 16:02:06.864][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-08-02 16:02:06.865][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-02 16:02:06.866][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-02 16:02:06.867][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-02 16:02:06.868][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-02 16:02:06.874][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-08-02 16:02:06.875][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-02 16:02:06.877][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-02 16:02:06.879][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-02 16:02:06.880][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-02 16:02:06.902][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-08-02 16:02:06.917][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-08-02 16:02:06.925][biodb::testThat]
biodb.INFO [2025-08-02 16:02:06.926][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-08-02 16:02:06.927][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-02 16:02:06.928][biodb::testThat]
biodb.TRACE[2025-08-02 16:02:06.932][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[2025-08-02 16:02:06.934][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-08-02 16:02:06.937][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-08-02 16:02:06.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-02 16:02:06.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:06.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:06.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:06.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:06.961][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:06.962][FUN] Functions in observer BiodbConfig: [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[2025-08-02 16:02:06.974][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:06.975][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:06.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:06.977][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:06.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:06.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:06.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:06.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:06.994][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:06.995][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:06.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:06.997][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.029][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:07.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:07.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.033][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.034][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.036][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.037][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.041][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-02 16:02:07.042][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-02 16:02:07.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.043][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.045][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-02 16:02:07.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-02 16:02:07.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.048][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.049][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.051][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.056][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.057][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.059][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.060][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.064][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.065][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.066][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.068][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.071][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.072][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.074][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.075][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.079][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.080][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.082][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.083][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.087][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.088][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.089][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.091][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.094][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-02 16:02:07.095][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-02 16:02:07.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.097][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.098][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-02 16:02:07.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-02 16:02:07.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.102][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-02 16:02:07.103][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-02 16:02:07.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.105][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.106][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-02 16:02:07.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-02 16:02:07.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.110][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-02 16:02:07.111][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-02 16:02:07.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.113][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.114][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-02 16:02:07.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-02 16:02:07.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.118][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.119][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.120][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.125][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:07.126][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:07.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.128][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.129][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:07.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:07.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.133][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-02 16:02:07.134][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-02 16:02:07.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.136][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.137][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-02 16:02:07.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-02 16:02:07.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.141][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-02 16:02:07.142][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-02 16:02:07.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.147][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.148][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-02 16:02:07.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-02 16:02:07.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.152][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-08-02 16:02:07.153][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:07.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.154][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.156][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-08-02 16:02:07.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:07.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.201][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.204][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.208][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.212][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-02 16:02:07.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-02 16:02:07.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.215][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-02 16:02:07.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-02 16:02:07.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.219][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-02 16:02:07.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-02 16:02:07.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.245][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.249][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.253][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.256][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.260][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.264][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.271][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:07.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:07.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.275][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:07.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:07.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.279][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:07.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:07.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.282][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-02 16:02:07.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-02 16:02:07.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.286][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-02 16:02:07.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-02 16:02:07.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.290][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-02 16:02:07.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-02 16:02:07.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.293][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-02 16:02:07.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-02 16:02:07.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.297][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-02 16:02:07.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-02 16:02:07.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.301][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-02 16:02:07.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-02 16:02:07.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.304][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-02 16:02:07.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-02 16:02:07.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.308][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-02 16:02:07.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-02 16:02:07.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.312][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-02 16:02:07.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-02 16:02:07.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.315][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-02 16:02:07.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-02 16:02:07.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.319][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-02 16:02:07.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-02 16:02:07.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.323][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-02 16:02:07.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-02 16:02:07.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.327][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.330][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.334][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.349][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:07.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:07.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.352][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:07.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:07.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:07.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:07.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.360][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.364][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.367][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.371][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:07.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:07.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.375][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:07.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:07.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.378][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:07.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:07.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.382][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-02 16:02:07.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-02 16:02:07.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.386][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-02 16:02:07.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-02 16:02:07.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.389][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-02 16:02:07.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-02 16:02:07.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.393][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-08-02 16:02:07.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-02 16:02:07.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.431][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-02 16:02:07.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-02 16:02:07.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-02 16:02:07.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-02 16:02:07.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.438][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-02 16:02:07.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-02 16:02:07.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.442][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-08-02 16:02:07.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-02 16:02:07.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.462][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:07.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:07.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:07.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:07.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:07.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:07.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:07.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:07.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:07.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:07.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.480][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-02 16:02:07.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-02 16:02:07.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.484][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-02 16:02:07.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-02 16:02:07.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.492][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-02 16:02:07.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-02 16:02:07.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-02 16:02:07.518][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-08-02 16:02:07.520][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-02 16:02:07.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-02 16:02:07.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.524][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-02 16:02:07.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-02 16:02:07.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.527][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-02 16:02:07.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-02 16:02:07.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.531][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-02 16:02:07.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-02 16:02:07.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.543][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-02 16:02:07.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-02 16:02:07.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.578][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-02 16:02:07.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-02 16:02:07.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.581][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-02 16:02:07.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-02 16:02:07.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.585][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-02 16:02:07.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-02 16:02:07.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.606][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.607][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.608][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:07.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:07.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.620][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:07.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:07.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.623][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:07.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:07.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.627][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:07.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:07.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.631][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:07.632][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:07.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.633][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.634][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:07.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:07.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.656][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.657][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.658][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:07.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.669][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.673][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.677][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.680][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.681][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.687][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.688][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:07.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.709][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.710][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.712][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-02 16:02:07.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.723][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.727][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.730][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.734][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.735][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.736][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.737][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.738][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:07.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.748][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:07.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:07.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.752][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:07.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:07.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.755][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:07.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:07.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.759][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:07.760][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:07.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.762][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.763][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:07.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:07.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.773][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-02 16:02:07.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-02 16:02:07.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.777][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-02 16:02:07.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-02 16:02:07.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.780][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-02 16:02:07.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-02 16:02:07.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.784][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-02 16:02:07.785][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-02 16:02:07.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.787][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.788][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-02 16:02:07.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-02 16:02:07.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.798][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-02 16:02:07.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-02 16:02:07.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.802][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-02 16:02:07.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-02 16:02:07.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.806][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-02 16:02:07.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-02 16:02:07.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.809][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-02 16:02:07.810][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-02 16:02:07.811][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.812][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.817][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-02 16:02:07.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-02 16:02:07.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.827][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.831][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.834][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.838][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.839][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.841][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.842][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-02 16:02:07.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.863][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.864][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.866][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:07.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.877][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:07.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:07.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.880][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:07.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:07.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.884][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:07.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:07.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.888][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:07.889][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:07.890][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.890][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.891][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:07.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:07.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.901][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.905][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.909][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.912][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.913][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.915][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.916][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:07.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.926][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.930][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.934][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.937][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.938][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.940][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.945][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:07.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.955][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-02 16:02:07.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-02 16:02:07.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.959][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-02 16:02:07.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-02 16:02:07.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.962][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-02 16:02:07.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-02 16:02:07.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.966][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-02 16:02:07.967][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-02 16:02:07.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.969][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.970][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-02 16:02:07.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-02 16:02:07.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.980][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-02 16:02:07.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-02 16:02:07.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.984][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-02 16:02:07.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-02 16:02:07.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.987][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-02 16:02:07.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-02 16:02:07.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.991][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-02 16:02:07.992][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-02 16:02:07.993][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.994][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:07.995][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-02 16:02:07.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-02 16:02:07.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:07.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.005][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-02 16:02:08.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-02 16:02:08.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.009][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-02 16:02:08.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-02 16:02:08.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.012][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-02 16:02:08.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-02 16:02:08.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.016][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-02 16:02:08.017][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-02 16:02:08.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.019][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.020][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-02 16:02:08.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-02 16:02:08.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.030][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-02 16:02:08.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-02 16:02:08.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.034][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-02 16:02:08.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-02 16:02:08.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.037][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-02 16:02:08.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-02 16:02:08.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.041][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-02 16:02:08.042][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-02 16:02:08.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.044][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.045][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-02 16:02:08.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-02 16:02:08.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.055][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-02 16:02:08.056][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-02 16:02:08.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.058][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.062][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-02 16:02:08.063][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-02 16:02:08.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.064][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.068][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-02 16:02:08.069][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-02 16:02:08.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.075][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.079][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-02 16:02:08.080][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-02 16:02:08.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.082][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.085][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:08.086][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-02 16:02:08.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.088][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.092][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:08.093][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-02 16:02:08.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.095][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.099][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:08.100][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-02 16:02:08.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.101][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.105][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:08.106][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-02 16:02:08.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.108][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.112][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-02 16:02:08.113][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-02 16:02:08.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.114][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.118][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-02 16:02:08.119][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-02 16:02:08.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.121][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.125][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-02 16:02:08.126][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-02 16:02:08.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.127][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.131][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-02 16:02:08.132][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-02 16:02:08.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.134][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.138][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:08.139][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-02 16:02:08.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.140][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.144][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:08.145][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-02 16:02:08.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.147][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.151][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:08.152][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:08.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.153][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.157][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:08.158][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-02 16:02:08.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.160][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.164][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:08.165][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:08.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.166][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.170][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-02 16:02:08.171][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-02 16:02:08.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.173][ef$get] fields variable is a list.
biodb.INFO [2025-08-02 16:02:08.179][biodb::testThat]
biodb.INFO [2025-08-02 16:02:08.180][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-02 16:02:08.181][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-02 16:02:08.182][biodb::testThat]
biodb.DEBUG[2025-08-02 16:02:08.199][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-02 16:02:08.201][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-02 16:02:08.204][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-02 16:02:08.231][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-02 16:02:08.232][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-02 16:02:08.233][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-02 16:02:08.268][biodb::testThat]
biodb.INFO [2025-08-02 16:02:08.269][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-02 16:02:08.270][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-02 16:02:08.271][biodb::testThat]
biodb.TRACE[2025-08-02 16:02:08.274][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:08.275][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:08.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.277][ef$get] fields variable is a list.
biodb.DEBUG[2025-08-02 16:02:08.278][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-08-02 16:02:08.297][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-02 16:02:08.345][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-02 16:02:08.347][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-02 16:02:08.348][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-02 16:02:08.349][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-02 16:02:08.361][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-02 16:02:08.384][biodb::testThat]
biodb.INFO [2025-08-02 16:02:08.385][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-08-02 16:02:08.386][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-02 16:02:08.387][biodb::testThat]
biodb.DEBUG[2025-08-02 16:02:08.393][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-02 16:02:08.394][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-02 16:02:08.395][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-02 16:02:08.396][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-02 16:02:08.398][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-02 16:02:08.399][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-02 16:02:08.410][biodb::testThat]
biodb.INFO [2025-08-02 16:02:08.411][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-08-02 16:02:08.412][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-02 16:02:08.413][biodb::testThat]
biodb.DEBUG[2025-08-02 16:02:08.417][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-02 16:02:08.418][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-02 16:02:08.419][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-02 16:02:08.420][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-02 16:02:08.421][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-02 16:02:08.422][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-02 16:02:08.438][biodb::testThat]
biodb.INFO [2025-08-02 16:02:08.439][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-02 16:02:08.440][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-02 16:02:08.441][biodb::testThat]
biodb.INFO [2025-08-02 16:02:08.453][biodb::testThat]
biodb.INFO [2025-08-02 16:02:08.454][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-02 16:02:08.455][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-02 16:02:08.456][biodb::testThat]
biodb.INFO [2025-08-02 16:02:08.468][biodb::testThat]
biodb.INFO [2025-08-02 16:02:08.469][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-02 16:02:08.470][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-02 16:02:08.471][biodb::testThat]
biodb.INFO [2025-08-02 16:02:08.483][biodb::testThat]
biodb.INFO [2025-08-02 16:02:08.484][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-02 16:02:08.485][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-02 16:02:08.486][biodb::testThat]
biodb.TRACE[2025-08-02 16:02:08.510][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:08.511][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:08.511][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.512][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.513][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-02 16:02:08.514][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-02 16:02:08.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.516][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.517][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:08.518][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:08.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.520][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.521][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-02 16:02:08.522][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-02 16:02:08.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.523][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.524][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-02 16:02:08.525][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-02 16:02:08.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.527][ef$get] fields variable is a list.
biodb.TRACE[2025-08-02 16:02:08.528][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:08.529][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-02 16:02:08.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-02 16:02:08.531][ef$get] fields variable is a list.
biodb.INFO [2025-08-02 16:02:08.532][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-02 16:02:08.533][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-08-02 16:02:08.534][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-02 16:02:08.534][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-02 16:02:08.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-02 16:02:08.540][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-02 16:02:08.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-02 16:02:08.541][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-02 16:02:08.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]

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

[ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.15.1’
* 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:
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
   5.       └─base::vapply(id, fct, FUN.VALUE = "")
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  
  [ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.15.1’
** 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)